libpdb-redo →
3.0.4-2 →
armhf → 2023-01-07 11:01:32
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| libpdb-redo 3.0.4-2 (armhf) Sat, 07 Jan 2023 10:38:44 +0000 |
+==============================================================================+
Package: libpdb-redo
Version: 3.0.4-2
Source Version: 3.0.4-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-fecd0614-a1e8-4c28-a107-1c1b176fdb76' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.9 MB in 30s (923 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'libpdb-redo' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/libpdb-redo.git
Please use:
git clone https://salsa.debian.org/med-team/libpdb-redo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 871 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main libpdb-redo 3.0.4-2 (dsc) [2277 B]
Get:2 http://172.17.4.1/private bookworm-staging/main libpdb-redo 3.0.4-2 (tar) [864 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main libpdb-redo 3.0.4-2 (diff) [4740 B]
Fetched 871 kB in 0s (3271 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libpdb-redo-xZMyZt/libpdb-redo-3.0.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libpdb-redo-xZMyZt' 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-xpenve/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-xpenve/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-xpenve/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-xpenve/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2796 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales 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 35 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-xpenve/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 (21.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12958 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libcifpp-dev (>= 5.0.4), cmake, libnewuoa-dev, pkg-config, libgsl-dev, libboost-dev, libboost-regex-dev, libclipper-dev, zlib1g-dev, libccp4-dev (>= 6.5.1-5)
Filtered Build-Depends: debhelper-compat (= 13), libcifpp-dev (>= 5.0.4), cmake, libnewuoa-dev, pkg-config, libgsl-dev, libboost-dev, libboost-regex-dev, libclipper-dev, zlib1g-dev, libccp4-dev (>= 6.5.1-5)
dpkg-deb: building package 'sbuild-build-depends-libpdb-redo-dummy' in '/<<BUILDDIR>>/resolver-xpenve/apt_archive/sbuild-build-depends-libpdb-redo-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-libpdb-redo-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-xpenve/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Sources [575 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ Packages [661 B]
Fetched 2569 B in 1s (3404 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install libpdb-redo 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 libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz fftw-dev fftw2 file
gettext gettext-base groff-base icu-devtools intltool-debian
libarchive-zip-perl libarchive13 libboost-dev libboost-regex-dev
libboost-regex1.74-dev libboost-regex1.74.0 libboost1.74-dev libbrotli1
libbsd0 libccp4-data libccp4-dev libccp4c0 libccp4f0 libcifpp-data
libcifpp-dev libcifpp5 libclipper-dev libclipper2 libcurl4 libdebhelper-perl
libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1
libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27
libgslcblas0 libhwloc-plugins libhwloc15 libibverbs1 libicu-dev libicu72
libjsoncpp25 libmagic-mgc libmagic1 libmd0 libmmdb2-0 libmmdb2-dev libmunge2
libnewuoa-dev libnewuoa0 libnghttp2-14 libnl-3-200 libnl-route-3-200
libopenmpi3 libpciaccess0 libpipeline1 libpkgconf3 libpmix2 libproc2-0
libpsl5 librdmacm1 librhash0 librtmp1 libssh2-1 libsub-override-perl libtool
libuchardet0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6
libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 pkg-config pkgconf
pkgconf-bin po-debconf procps sfftw-dev sfftw2 zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
elpa-cmake-mode ninja-build dh-make mpi-defaults-bin gettext-doc
libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.74-doc
libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
libboost-context1.74-dev libboost-contract1.74-dev
libboost-coroutine1.74-dev libboost-date-time1.74-dev
libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-serialization1.74-dev
libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev
libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev
libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev
libboost-nowide1.74-dev libclipper-doc gsl-ref-psdoc | gsl-doc-pdf
| gsl-doc-info | gsl-ref-html icu-doc pciutils libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser opencl-icd
libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl ibverbs-providers
publicsuffix libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz fftw-dev fftw2 file
gettext gettext-base groff-base icu-devtools intltool-debian
libarchive-zip-perl libarchive13 libboost-dev libboost-regex-dev
libboost-regex1.74-dev libboost-regex1.74.0 libboost1.74-dev libbrotli1
libbsd0 libccp4-data libccp4-dev libccp4c0 libccp4f0 libcifpp-data
libcifpp-dev libcifpp5 libclipper-dev libclipper2 libcurl4 libdebhelper-perl
libelf1 libevent-core-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1
libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27
libgslcblas0 libhwloc-plugins libhwloc15 libibverbs1 libicu-dev libicu72
libjsoncpp25 libmagic-mgc libmagic1 libmd0 libmmdb2-0 libmmdb2-dev libmunge2
libnewuoa-dev libnewuoa0 libnghttp2-14 libnl-3-200 libnl-route-3-200
libopenmpi3 libpciaccess0 libpipeline1 libpkgconf3 libpmix2 libproc2-0
libpsl5 librdmacm1 librhash0 librtmp1 libssh2-1 libsub-override-perl libtool
libuchardet0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6
libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 pkg-config pkgconf
pkgconf-bin po-debconf procps sbuild-build-depends-libpdb-redo-dummy
sfftw-dev sfftw2 zlib1g-dev
0 upgraded, 101 newly installed, 0 to remove and 35 not upgraded.
Need to get 58.5 MB of archives.
After this operation, 364 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-xpenve/apt_archive ./ sbuild-build-depends-libpdb-redo-dummy 0.invalid.0 [948 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libproc2-0 armhf 2:4.0.2-3 [53.6 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:4.0.2-3 [679 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.2-1 [293 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.51.0-1 [60.5 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.87.0-1 [332 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.2-1+rpi1 [125 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.25.1-1 [2026 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.25.1-1 [3859 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-5 [517 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.11.4 [942 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-5+b1 [125 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-5+b1 [57.6 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libnl-3-200 armhf 3.7.0-0.2 [55.0 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libnl-route-3-200 armhf 3.7.0-0.2 [152 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libibverbs1 armhf 42.0-1 [53.7 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf librdmacm1 armhf 42.0-1 [60.3 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libfabric1 armhf 1.11.0-3 [310 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libhwloc15 armhf 2.9.0-1 [124 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libmunge2 armhf 0.5.14-6 [18.6 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libpciaccess0 armhf 0.17-2 [48.8 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.3-3 [292 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.3-3 [687 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libxnvctrl0 armhf 510.85.02-2 [26.6 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf ocl-icd-libopencl1 armhf 2.3.1-1 [40.3 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libhwloc-plugins armhf 2.9.0-1 [16.0 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libpmix2 armhf 4.2.2-1 [530 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libopenmpi3 armhf 4.1.4-3+rpi1 [1795 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf fftw2 armhf 2.1.5-6 [184 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf fftw-dev armhf 2.1.5-6 [212 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 72.1-3 [175 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-18.1 [9509 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b4 [4824 B]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-18.1 [420 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 72.1-3 [9959 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-18.1 [525 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libboost-regex-dev armhf 1.74.0.3+b4 [4876 B]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libccp4-data all 8.0.0-2 [62.3 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libccp4c0 armhf 8.0.0-2 [74.3 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-10+rpi1 [238 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libmmdb2-0 armhf 2.0.22-1 [269 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libccp4f0 armhf 8.0.0-2 [185 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libccp4-dev armhf 8.0.0-2 [42.8 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libcifpp-data all 5.0.5-6 [452 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libcifpp5 armhf 5.0.5-6 [669 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [901 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libcifpp-dev armhf 5.0.5-6 [85.7 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf sfftw2 armhf 2.1.5-6 [186 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libclipper2 armhf 2.1.20201109-1 [1069 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libmmdb2-dev armhf 2.0.22-1 [92.9 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf sfftw-dev armhf 2.1.5-6 [214 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libclipper-dev armhf 2.1.20201109-1 [82.6 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-3 [81.4 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libgsl27 armhf 2.7.1+dfsg-3 [758 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-3 [958 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libnewuoa0 armhf 0.1.2-1 [15.7 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libnewuoa-dev armhf 0.1.2-1 [7504 B]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libpkgconf3 armhf 1.8.0-12 [31.0 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf pkgconf-bin armhf 1.8.0-12 [27.6 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf pkgconf armhf 1.8.0-12 [25.6 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 1.8.0-12 [13.5 kB]
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libboost-regex1.74.0:armhf (1.74.0-18.1) ...
Setting up libproc2-0:armhf (2:4.0.2-3) ...
Setting up libhwloc15:armhf (2.9.0-1) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up libmmdb2-dev (2.0.22-1) ...
Setting up autopoint (0.21-10) ...
Setting up libjsoncpp25:armhf (1.9.5-4) ...
Setting up icu-devtools (72.1-3) ...
Setting up libccp4c0:armhf (8.0.0-2) ...
Setting up pkgconf-bin (1.8.0-12) ...
Setting up libcifpp-data (5.0.5-6) ...
Setting up libgfortran5:armhf (12.2.0-10+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ...
Setting up libmd0:armhf (1.0.4-2) ...
Setting up ocl-icd-libopencl1:armhf (2.3.1-1) ...
Setting up librhash0:armhf (1.4.3-3) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up procps (2:4.0.2-3) ...
Setting up libnl-3-200:armhf (3.7.0-0.2) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up cmake-data (3.25.1-1) ...
Setting up libboost-dev:armhf (1.74.0.3+b4) ...
Setting up libbsd0:armhf (0.11.7-1) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libicu-dev:armhf (72.1-3) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.1) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-5+b1) ...
Setting up libccp4f0:armhf (8.0.0-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-10) ...
Setting up libgsl-dev (2.7.1+dfsg-3) ...
Setting up libccp4-dev:armhf (8.0.0-2) ...
Setting up libtool (2.4.7-5) ...
Setting up libarchive13:armhf (3.6.2-1) ...
Setting up libnewuoa-dev (0.1.2-1) ...
Setting up pkgconf:armhf (1.8.0-12) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libnl-route-3-200:armhf (3.7.0-0.2) ...
Setting up libcifpp5:armhf (5.0.5-6) ...
Setting up dh-autoreconf (20) ...
Setting up pkg-config:armhf (1.8.0-12) ...
Setting up dh-strip-nondeterminism (1.13.0-2) ...
Setting up dwz (0.15-1) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0-18.1) ...
Setting up groff-base (1.22.4-9) ...
Setting up libcurl4:armhf (7.87.0-1) ...
Setting up libx11-6:armhf (2:1.8.3-3) ...
Setting up libboost-regex-dev:armhf (1.74.0.3+b4) ...
Setting up libibverbs1:armhf (42.0-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxnvctrl0:armhf (510.85.02-2) ...
Setting up libcifpp-dev:armhf (5.0.5-6) ...
Setting up cmake (3.25.1-1) ...
Setting up librdmacm1:armhf (42.0-1) ...
Setting up debhelper (13.11.4) ...
Setting up libhwloc-plugins:armhf (2.9.0-1) ...
Setting up libfabric1:armhf (1.11.0-3) ...
Setting up libpmix2:armhf (4.2.2-1) ...
Setting up libopenmpi3:armhf (4.1.4-3+rpi1) ...
Setting up sfftw2 (2.1.5-6) ...
Setting up fftw2 (2.1.5-6) ...
Setting up sfftw-dev (2.1.5-6) ...
Setting up libclipper2:armhf (2.1.20201109-1) ...
Setting up fftw-dev (2.1.5-6) ...
Setting up libclipper-dev:armhf (2.1.20201109-1) ...
Setting up sbuild-build-depends-libpdb-redo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.36-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.39.50.20221208-5+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-10+rpi1 gcc-12_12.2.0-10+rpi1 libc6-dev_2.36-6+rpi1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 linux-libc-dev_6.0.12-1+rpi1
Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2-2 binutils_2.39.50.20221208-5+rpi1 binutils-arm-linux-gnueabihf_2.39.50.20221208-5+rpi1 binutils-common_2.39.50.20221208-5+rpi1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.25.1-1 cmake-data_3.25.1-1 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.4 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.40-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 fftw-dev_2.1.5-6 fftw2_2.1.5-6 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-10+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-10+rpi1 gcc-12-base_12.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-10 gettext-base_0.21-10 gnupg_2.2.40-1 gnupg-l10n_2.2.40-1 gnupg-utils_2.2.40-1 gpg_2.2.40-1 gpg-agent_2.2.40-1 gpg-wks-client_2.2.40-1 gpg-wks-server_2.2.40-1 gpgconf_2.2.40-1 gpgsm_2.2.40-1 gpgv_2.2.40-1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 icu-devtools_72.1-3 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-1 libacl1_2.3.1-2 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libarchive13_3.6.2-1 libasan8_12.2.0-10+rpi1 libassuan0_2.5.5-5 libatomic1_12.2.0-10+rpi1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39.50.20221208-5+rpi1 libblkid1_2.38.1-4 libboost-dev_1.74.0.3+b4 libboost-regex-dev_1.74.0.3+b4 libboost-regex1.74-dev_1.74.0-18.1 libboost-regex1.74.0_1.74.0-18.1 libboost1.74-dev_1.74.0-18.1 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.36-6+rpi1 libc-dev-bin_2.36-6+rpi1 libc6_2.36-6+rpi1 libc6-dev_2.36-6+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-10+rpi1 libccp4-data_8.0.0-2 libccp4-dev_8.0.0-2 libccp4c0_8.0.0-2 libccp4f0_8.0.0-2 libcifpp-data_5.0.5-6 libcifpp-dev_5.0.5-6 libcifpp5_5.0.5-6 libclipper-dev_2.1.20201109-1 libclipper2_2.1.20201109-1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libctf-nobfd0_2.39.50.20221208-5+rpi1 libctf0_2.39.50.20221208-5+rpi1 libcurl4_7.87.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.265 libdebhelper-perl_13.11.4 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libevent-core-2.1-7_2.1.12-stable-5+b1 libevent-pthreads-2.1-7_2.1.12-stable-5+b1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfabric1_1.11.0-3 libfakeroot_1.29-1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-2 libgcc-12-dev_12.2.0-10+rpi1 libgcc-s1_12.2.0-10+rpi1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-10+rpi1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-10+rpi1 libgpg-error0_1.46-1 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.20.1-1 libhogweed6_3.8.1-2 libhwloc-plugins_2.9.0-1 libhwloc15_2.9.0-1 libibverbs1_42.0-1 libicu-dev_72.1-3 libicu72_72.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjansson4_2.14-2 libjsoncpp25_1.9.5-4 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 libksba8_1.6.2-4 libldap-2.5-0_2.5.13+dfsg-2+rpi1+b1 liblz4-1_1.9.4-1+rpi1 liblzma5_5.4.0-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmmdb2-0_2.0.22-1 libmmdb2-dev_2.0.22-1 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libmunge2_0.5.14-6 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnewuoa-dev_0.1.2-1 libnewuoa0_0.1.2-1 libnghttp2-14_1.51.0-1 libnl-3-200_3.7.0-0.2 libnl-route-3-200_3.7.0-0.2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenmpi3_4.1.4-3+rpi1 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpciaccess0_0.17-2 libpcre2-8-0_10.40-3 libpcre3_2:8.39-14 libperl5.36_5.36.0-6 libpipeline1_1.5.7-1 libpkgconf3_1.8.0-12 libpmix2_4.2.2-1 libproc2-0_2:4.0.2-3 libpsl5_0.21.0-1.2 librdmacm1_42.0-1 libreadline8_8.2-1.2 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-4 libsqlite3-0_3.40.0-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.7-1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.2-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_252.2-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-4 libuv1_1.44.2-1+rpi1 libx11-6_2:1.8.3-3 libx11-data_2:1.8.3-3 libxau6_1:1.0.9-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.14+dfsg-1.1 libxnvctrl0_510.85.02-2 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_6.0.12-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-4 nano_7.1-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.4 ocl-icd-libopencl1_2.3.1-1 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-6 perl-base_5.36.0-6 perl-modules-5.36_5.36.0-6 pinentry-curses_1.2.1-1 pkg-config_1.8.0-12 pkgconf_1.8.0-12 pkgconf-bin_1.8.0-12 po-debconf_1.0.21+nmu1 procps_2:4.0.2-3 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.2 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libpdb-redo-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sfftw-dev_2.1.5-6 sfftw2_2.1.5-6 sgml-base_1.31 sysvinit-utils_3.05-7 tar_1.34+dfsg-1 tzdata_2022f-1 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.llgm8mTk/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 30 08:18:55 2022 UTC
gpgv: using RSA key A72B6824226BB407E24B9E80587503EC7AE7EDCE
gpgv: issuer "maarten@hekkelman.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./libpdb-redo_3.0.4-2.dsc
dpkg-source: info: extracting libpdb-redo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking libpdb-redo_3.0.4.orig.tar.gz
dpkg-source: info: unpacking libpdb-redo_3.0.4-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix-examples.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-fecd0614-a1e8-4c28-a107-1c1b176fdb76
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package libpdb-redo
dpkg-buildpackage: info: source version 3.0.4-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON ..
-- The CXX compiler identification is GNU 12.2.0
-- The C compiler identification is GNU 12.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.0")
Using resources not possible since mrc was not found
-- Looking for ccp4/ccp4_general.h - /usr/include
-- Found CCP4: /usr/lib/arm-linux-gnueabihf/libccp4c.so
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for clipper/clipper.h - /usr/include
-- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-core.so
-- FFTW2 libraries - /usr/lib/libsfftw.so
-- - /usr/lib/libsrfftw.so
-- FFTW2 header directory - /usr/include
-- Performing Test _LINKING_WITH_CLIPPER_CORE
-- Performing Test _LINKING_WITH_CLIPPER_CORE - Success
-- Looking for clipper/clipper-ccp4.h - /usr/include
-- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-ccp4.so
-- Looking for clipper/clipper-contrib.h - /usr/include
-- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-contrib.so
-- CCP4 include directory: /usr/include
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13")
-- Found Boost: /usr/lib/arm-linux-gnueabihf/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: regex
-- Checking for module 'gsl'
-- Found gsl, version 2.7.1
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
FETCHCONTENT_FULLY_DISCONNECTED
PDB_REDO_BUILD_TESTS
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/pdb-redo.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 14%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o
[ 14%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o
[ 21%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -MF CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -c /<<PKGBUILDDIR>>/src/AtomShape.cpp
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -c /<<PKGBUILDDIR>>/src/BondMap.cpp
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -c /<<PKGBUILDDIR>>/src/ClipperWrapper.cpp
[ 28%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Compound.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -c /<<PKGBUILDDIR>>/src/Compound.cpp
[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -c /<<PKGBUILDDIR>>/src/DistanceMap.cpp
[ 42%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -MF CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -c /<<PKGBUILDDIR>>/src/MapMaker.cpp
[ 50%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -c /<<PKGBUILDDIR>>/src/Ramachandran.cpp
/<<PKGBUILDDIR>>/src/MapMaker.cpp: In member function ‘void pdb_redo::MapMaker<FTYPE>::fixMTZ() [with FTYPE = float]’:
/<<PKGBUILDDIR>>/src/MapMaker.cpp:1114:22: note: parameter passing for argument of type ‘clipper::datatypes::F_phi<float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
1114 | auto mFo = mFbData[ih] - mFdData[ih];
| ^~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/cif++/forward_decl.hpp:30,
from /usr/include/cif++/datablock.hpp:29,
from /usr/include/cif++/file.hpp:31,
from /usr/include/cif++.hpp:30,
from /<<PKGBUILDDIR>>/include/pdb-redo/ClipperWrapper.hpp:29,
from /<<PKGBUILDDIR>>/src/DistanceMap.cpp:32:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator<clipper::RTop_orth>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<clipper::RTop_orth>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator<clipper::RTop_orth>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<clipper::RTop_orth*, std::vector<clipper::RTop_orth> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 57%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -c /<<PKGBUILDDIR>>/src/ResolutionCalculator.cpp
[ 64%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -MF CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -c /<<PKGBUILDDIR>>/src/SkipList.cpp
[ 71%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -c /<<PKGBUILDDIR>>/src/Statistics.cpp
In file included from /usr/include/c++/12/vector:70,
from /usr/include/clipper/ccp4/ccp4_utils.h:49,
from /usr/include/clipper/clipper-ccp4.h:7,
from /<<PKGBUILDDIR>>/src/MapMaker.cpp:31:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void clipper::Array2d<T>::resize(const int&, const int&, const T&) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:379:40,
inlined from ‘clipper::Matrix<T>::Matrix(const int&, const int&, T) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:406:27,
inlined from ‘clipper::BasisFn_base::Fderiv::Fderiv(const int&)’ at /usr/include/clipper/core/resol_fn.h:80:43,
inlined from ‘clipper::BasisFn_base::BasisFn_base(const int&)’ at /usr/include/clipper/core/resol_fn.h:86:46,
inlined from ‘clipper::BasisFn_spline::BasisFn_spline(const clipper::HKL_data_base&, const int&, clipper::ftype)’ at /usr/include/clipper/core/resol_basisfn.h:136:120:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algobase.h:64,
from /usr/include/c++/12/string:50,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<PKGBUILDDIR>>/src/Statistics.cpp:27:
/usr/include/c++/12/bits/stl_pair.h: In instantiation of ‘constexpr std::pair<typename std::__strip_reference_wrapper<typename std::decay<_Tp>::type>::__type, typename std::__strip_reference_wrapper<typename std::decay<_Tp2>::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double; _T2 = double; typename __strip_reference_wrapper<typename decay<_Tp2>::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper<typename decay<_Tp>::type>::__type = double; typename decay<_Tp>::type = double]’:
/<<PKGBUILDDIR>>/src/Statistics.cpp:545:41: required from here
/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
741 | make_pair(_T1&& __x, _T2&& __y)
| ^~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator<clipper::Atom>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<clipper::Atom>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator<clipper::Atom>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<clipper::Atom*, std::vector<clipper::Atom> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/functional:64,
from /usr/include/cif++/condition.hpp:30,
from /usr/include/cif++/category.hpp:33,
from /usr/include/cif++/datablock.hpp:31,
from /usr/include/cif++/file.hpp:31,
from /usr/include/cif++.hpp:30,
from /<<PKGBUILDDIR>>/src/Statistics.cpp:30:
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o -c /<<PKGBUILDDIR>>/src/Symmetry-2.cpp
[ 85%] Building CXX object CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o -c /<<PKGBUILDDIR>>/src/Minimizer.cpp
In file included from /usr/include/c++/12/vector:70,
from /usr/include/cif++/forward_decl.hpp:30,
from /usr/include/cif++/datablock.hpp:29:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {pdb_redo::ResidueStatistics}; _Tp = pdb_redo::ResidueStatistics; _Alloc = std::allocator<pdb_redo::ResidueStatistics>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::ResidueStatistics>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const clipper::Coord_grid&, double&}; _Tp = pdb_redo::AtomGridData; _Alloc = std::allocator<pdb_redo::AtomGridData>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::AtomGridData>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/12/regex:53,
from /usr/include/cif++/condition.hpp:32:
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const clipper::Coord_grid&>, std::tuple<>}; _Key = clipper::Coord_grid; _Val = std::pair<const clipper::Coord_grid, double>; _KeyOfValue = std::_Select1st<std::pair<const clipper::Coord_grid, double> >; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator<std::pair<const clipper::Coord_grid, double> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<clipper::Coord_grid, std::pair<const clipper::Coord_grid, double>, std::_Select1st<std::pair<const clipper::Coord_grid, double> >, pdb_redo::StatsCollector::cmpGPt, std::allocator<std::pair<const clipper::Coord_grid, double> > >::const_iterator’ changed in GCC 7.1
In file included from /usr/include/c++/12/regex:54:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = clipper::Coord_grid; _Tp = double; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator<std::pair<const clipper::Coord_grid, double> >]’,
inlined from ‘pdb_redo::StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const::<lambda(clipper::Xmap_base::Map_reference_coord&)>’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:968:32,
inlined from ‘void pdb_redo::iterateGrid(const clipper::Coord_orth&, float, const clipper::Xmap<FTYPE>&, F&&) [with F = StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const::<lambda(clipper::Xmap_base::Map_reference_coord&)>; FTYPE = float]’ at /<<PKGBUILDDIR>>/include/pdb-redo/Statistics.hpp:76:9,
inlined from ‘void pdb_redo::StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:955:14:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<clipper::Coord_grid, std::pair<const clipper::Coord_grid, double>, std::_Select1st<std::pair<const clipper::Coord_grid, double> >, pdb_redo::StatsCollector::cmpGPt, std::allocator<std::pair<const clipper::Coord_grid, double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const clipper::Coord_grid&, double&}; _Tp = pdb_redo::AtomGridData; _Alloc = std::allocator<pdb_redo::AtomGridData>]’,
inlined from ‘pdb_redo::StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const::<lambda(clipper::Xmap_base::Map_reference_coord&)>’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:969:29,
inlined from ‘void pdb_redo::iterateGrid(const clipper::Coord_orth&, float, const clipper::Xmap<FTYPE>&, F&&) [with F = StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const::<lambda(clipper::Xmap_base::Map_reference_coord&)>; FTYPE = float]’ at /<<PKGBUILDDIR>>/include/pdb-redo/Statistics.hpp:76:9,
inlined from ‘void pdb_redo::StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:955:14:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::AtomGridData*, std::vector<pdb_redo::AtomGridData> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘pdb_redo::StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const::<lambda(clipper::Xmap_base::Map_reference_coord&)>’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:973:42,
inlined from ‘void pdb_redo::iterateGrid(const clipper::Coord_orth&, float, const clipper::Xmap<FTYPE>&, F&&) [with F = StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const::<lambda(clipper::Xmap_base::Map_reference_coord&)>; FTYPE = float]’ at /<<PKGBUILDDIR>>/include/pdb-redo/Statistics.hpp:76:9,
inlined from ‘void pdb_redo::StatsCollector::sumDensity(std::vector<pdb_redo::AtomData>&, GridPtDataMap&, std::map<std::__cxx11::basic_string<char>, std::vector<double> >&) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:955:14:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {cif::mm::atom&, float&}; _Tp = pdb_redo::AtomData; _Alloc = std::allocator<pdb_redo::AtomData>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::AtomData>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {cif::mm::atom&, float&}; _Tp = pdb_redo::AtomData; _Alloc = std::allocator<pdb_redo::AtomData>]’,
inlined from ‘std::vector<pdb_redo::ResidueStatistics> pdb_redo::StatsCollector::collect(const residue_list&, pdb_redo::BoundingBox&, bool) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:665:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::AtomData*, std::vector<pdb_redo::AtomData> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pdb_redo::ResidueStatistics}; _Tp = pdb_redo::ResidueStatistics; _Alloc = std::allocator<pdb_redo::ResidueStatistics>]’,
inlined from ‘std::vector<pdb_redo::ResidueStatistics> pdb_redo::StatsCollector::collect(const residue_list&, pdb_redo::BoundingBox&, bool) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:819:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::ResidueStatistics*, std::vector<pdb_redo::ResidueStatistics> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pdb_redo::ResidueStatistics}; _Tp = pdb_redo::ResidueStatistics; _Alloc = std::allocator<pdb_redo::ResidueStatistics>]’,
inlined from ‘std::vector<pdb_redo::ResidueStatistics> pdb_redo::StatsCollector::collect(const residue_list&, pdb_redo::BoundingBox&, bool) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:838:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::ResidueStatistics*, std::vector<pdb_redo::ResidueStatistics> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = std::pair<double, double>; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > >]’,
inlined from ‘void pdb_redo::StatsCollector::initialize()’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:402:21:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {cif::mm::atom&, float&}; _Tp = pdb_redo::AtomData; _Alloc = std::allocator<pdb_redo::AtomData>]’,
inlined from ‘void pdb_redo::StatsCollector::initialize()’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:467:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::AtomData*, std::vector<pdb_redo::AtomData> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void pdb_redo::StatsCollector::initialize()’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:483:7:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘void pdb_redo::StatsCollector::initialize()’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:483:7:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = std::pair<double, double>; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > >]’,
inlined from ‘void pdb_redo::StatsCollector::initialize()’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:545:23:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::pair<double, double> > > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {cif::mm::atom&, float&}; _Tp = pdb_redo::AtomData; _Alloc = std::allocator<pdb_redo::AtomData>]’,
inlined from ‘virtual pdb_redo::ResidueStatistics pdb_redo::StatsCollector::collect(const std::vector<cif::mm::atom>&) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:888:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::AtomData*, std::vector<pdb_redo::AtomData> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = clipper::Coord_grid; _Tp = double; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator<std::pair<const clipper::Coord_grid, double> >]’,
inlined from ‘void pdb_redo::StatsCollector::collectSums(std::vector<pdb_redo::AtomData>&, GridPtDataMap&) const’ at /<<PKGBUILDDIR>>/src/Statistics.cpp:998:36:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<clipper::Coord_grid, std::pair<const clipper::Coord_grid, double>, std::_Select1st<std::pair<const clipper::Coord_grid, double> >, pdb_redo::StatsCollector::cmpGPt, std::allocator<std::pair<const clipper::Coord_grid, double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/cif++/forward_decl.hpp:30,
from /usr/include/cif++/datablock.hpp:29,
from /usr/include/cif++/file.hpp:31,
from /usr/include/cif++.hpp:30,
from /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:30:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::Coord_orth}; _Tp = clipper::Coord_orth; _Alloc = std::allocator<clipper::Coord_orth>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<clipper::Coord_orth>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::Coord_orth}; _Tp = clipper::Coord_orth; _Alloc = std::allocator<clipper::Coord_orth>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = clipper::Coord_orth; _Alloc = std::allocator<clipper::Coord_orth>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘clipper::Coord_orth pdb_redo::CalculateOffsetForCell(const cif::mm::structure&, const clipper::Spacegroup&, const clipper::Cell&)’ at /<<PKGBUILDDIR>>/src/Symmetry-2.cpp:59:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<clipper::Coord_orth*, std::vector<clipper::Coord_orth> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator<clipper::RTop_orth>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<clipper::RTop_orth>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator<clipper::RTop_orth>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<clipper::RTop_orth*, std::vector<clipper::RTop_orth> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 92%] Building CXX object CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_REGEX_DYN_LINK -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -fPIC -std=gnu++17 -MD -MT CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o -c /<<PKGBUILDDIR>>/src/Restraints.cpp
In file included from /usr/include/c++/12/vector:70,
from /usr/include/cif++/forward_decl.hpp:30,
from /usr/include/cif++/datablock.hpp:29,
from /usr/include/cif++/file.hpp:31,
from /usr/include/cif++.hpp:30,
from /<<PKGBUILDDIR>>/src/Restraints.cpp:34:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void clipper::Array2d<T>::resize(const int&, const int&, const T&) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:379:40,
inlined from ‘clipper::Matrix<T>::Matrix(const int&, const int&, T) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:406:27,
inlined from ‘std::vector<_Ch_type> clipper::Matrix<T>::eigen(bool) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:614:10:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/c++/12/bits/random.h:34,
from /usr/include/c++/12/random:49,
from /<<PKGBUILDDIR>>/src/Minimizer.cpp:35:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, float&, float&}; _Tp = pdb_redo::BondRestraint; _Alloc = std::allocator<pdb_redo::BondRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::BondRestraint>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, unsigned int, float&, float&}; _Tp = pdb_redo::BondRestraint; _Alloc = std::allocator<pdb_redo::BondRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::BondRestraint*, std::vector<pdb_redo::BondRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, float&, float&}; _Tp = pdb_redo::AngleRestraint; _Alloc = std::allocator<pdb_redo::AngleRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::AngleRestraint>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, float&, float&}; _Tp = pdb_redo::AngleRestraint; _Alloc = std::allocator<pdb_redo::AngleRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::AngleRestraint*, std::vector<pdb_redo::AngleRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float&, float&, int&}; _Tp = pdb_redo::TorsionRestraint; _Alloc = std::allocator<pdb_redo::TorsionRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::TorsionRestraint>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float}; _Tp = pdb_redo::ChiralVolumeRestraint; _Alloc = std::allocator<pdb_redo::ChiralVolumeRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::ChiralVolumeRestraint>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::vector<unsigned int, std::allocator<unsigned int> >, float&}; _Tp = pdb_redo::PlanarityRestraint; _Alloc = std::allocator<pdb_redo::PlanarityRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::PlanarityRestraint>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {pdb_redo::TransPeptideRestraint}; _Tp = pdb_redo::TransPeptideRestraint; _Alloc = std::allocator<pdb_redo::TransPeptideRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::TransPeptideRestraint>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {pdb_redo::PlanarityRestraint}; _Tp = pdb_redo::PlanarityRestraint; _Alloc = std::allocator<pdb_redo::PlanarityRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::PlanarityRestraint>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pdb_redo::PlanarityRestraint}; _Tp = pdb_redo::PlanarityRestraint; _Alloc = std::allocator<pdb_redo::PlanarityRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::PlanarityRestraint*, std::vector<pdb_redo::PlanarityRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int&, unsigned int&, double&, double}; _Tp = pdb_redo::NonBondedContactRestraint; _Alloc = std::allocator<pdb_redo::NonBondedContactRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::NonBondedContactRestraint>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float&}; _Tp = pdb_redo::ChiralVolumeRestraint; _Alloc = std::allocator<pdb_redo::ChiralVolumeRestraint>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<pdb_redo::ChiralVolumeRestraint>::iterator’ changed in GCC 7.1
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float&}; _Tp = pdb_redo::ChiralVolumeRestraint; _Alloc = std::allocator<pdb_redo::ChiralVolumeRestraint>]’,
inlined from ‘void pdb_redo::Minimizer::addLinkRestraints(const cif::mm::residue&, const cif::mm::residue&, const pdb_redo::Link&)’ at /<<PKGBUILDDIR>>/src/Minimizer.cpp:699:40:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::ChiralVolumeRestraint*, std::vector<pdb_redo::ChiralVolumeRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {pdb_redo::TransPeptideRestraint}; _Tp = pdb_redo::TransPeptideRestraint; _Alloc = std::allocator<pdb_redo::TransPeptideRestraint>]’,
inlined from ‘virtual void pdb_redo::Minimizer::addPolySection(const cif::mm::polymer&, int, int)’ at /<<PKGBUILDDIR>>/src/Minimizer.cpp:282:43:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::TransPeptideRestraint*, std::vector<pdb_redo::TransPeptideRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<unsigned int, double>}; _Tp = std::pair<unsigned int, double>; _Alloc = std::allocator<std::pair<unsigned int, double> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<unsigned int, double> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<unsigned int, double>}; _Tp = std::pair<unsigned int, double>; _Alloc = std::allocator<std::pair<unsigned int, double> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<unsigned int, double>; _Alloc = std::allocator<std::pair<unsigned int, double> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector<std::pair<unsigned int, double> >]’ at /usr/include/c++/12/bits/stl_iterator.h:743:22,
inlined from ‘_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<cif::mm::atom*, vector<cif::mm::atom> >; _OIter = back_insert_iterator<vector<pair<unsigned int, double> > >; _UnaryOperation = pdb_redo::Minimizer::addDensityMap(const XMap&, float)::<lambda(const cif::mm::atom&)>]’ at /usr/include/c++/12/bits/stl_algo.h:4263:12,
inlined from ‘virtual void pdb_redo::Minimizer::addDensityMap(const XMap&, float)’ at /<<PKGBUILDDIR>>/src/Minimizer.cpp:325:11:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<unsigned int, double>*, std::vector<std::pair<unsigned int, double> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float&, float&, int&}; _Tp = pdb_redo::TorsionRestraint; _Alloc = std::allocator<pdb_redo::TorsionRestraint>]’,
inlined from ‘virtual void pdb_redo::Minimizer::addResidue(const cif::mm::residue&)’ at /<<PKGBUILDDIR>>/src/Minimizer.cpp:176:35:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::TorsionRestraint*, std::vector<pdb_redo::TorsionRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float}; _Tp = pdb_redo::ChiralVolumeRestraint; _Alloc = std::allocator<pdb_redo::ChiralVolumeRestraint>]’,
inlined from ‘virtual void pdb_redo::Minimizer::addResidue(const cif::mm::residue&)’ at /<<PKGBUILDDIR>>/src/Minimizer.cpp:207:40:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::ChiralVolumeRestraint*, std::vector<pdb_redo::ChiralVolumeRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::vector<unsigned int, std::allocator<unsigned int> >, float&}; _Tp = pdb_redo::PlanarityRestraint; _Alloc = std::allocator<pdb_redo::PlanarityRestraint>]’,
inlined from ‘virtual void pdb_redo::Minimizer::addResidue(const cif::mm::residue&)’ at /<<PKGBUILDDIR>>/src/Minimizer.cpp:237:38:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::PlanarityRestraint*, std::vector<pdb_redo::PlanarityRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int&, unsigned int&, double&, double}; _Tp = pdb_redo::NonBondedContactRestraint; _Alloc = std::allocator<pdb_redo::NonBondedContactRestraint>]’,
inlined from ‘virtual void pdb_redo::Minimizer::Finish()’ at /<<PKGBUILDDIR>>/src/Minimizer.cpp:515:45:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pdb_redo::NonBondedContactRestraint*, std::vector<pdb_redo::NonBondedContactRestraint> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX shared library libpdb-redo.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libpdb-redo.so.3 -o libpdb-redo.so.3.0.4 "CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o" "CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o" "CMakeFiles/pdb-redo.dir/src/Compound.cpp.o" "CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o" "CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o" "CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o" "CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o" "CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o" "CMakeFiles/pdb-redo.dir/src/Symmetry-2.cpp.o" "CMakeFiles/pdb-redo.dir/src/Minimizer.cpp.o" "CMakeFiles/pdb-redo.dir/src/Restraints.cpp.o" /usr/lib/arm-linux-gnueabihf/libcifpp.so.5.0.5 /usr/lib/arm-linux-gnueabihf/libnewuoa.so.0.1.2 /usr/lib/arm-linux-gnueabihf/libclipper-ccp4.so /usr/lib/arm-linux-gnueabihf/libclipper-contrib.so /usr/lib/arm-linux-gnueabihf/libclipper-core.so /usr/lib/arm-linux-gnueabihf/libccp4c.so -lgsl -lgslcblas -lm /usr/lib/arm-linux-gnueabihf/libz.so -latomic /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.74.0
/usr/bin/cmake -E cmake_symlink_library libpdb-redo.so.3.0.4 libpdb-redo.so.3 libpdb-redo.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target pdb-redo
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_auto_test -a
cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j4
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
No tests were found!!!
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3.0.4
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets-none.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/AtomShape.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/BondMap.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/Compound.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/MapMaker.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/Minimizer.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/Ramachandran.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/ResolutionCalculator.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/Restraints.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/SkipList.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/Statistics.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/pdb-redo/Symmetry-2.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfig.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfigVersion.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/libpdb-redo.pc
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libpdb-redo3/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3.0.4 found in none of the libraries
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.0.4-2_armhf.deb'.
dpkg-deb: building package 'libpdb-redo3-dbgsym' in '../libpdb-redo3-dbgsym_3.0.4-2_armhf.deb'.
dpkg-deb: building package 'libpdb-redo3' in '../libpdb-redo3_3.0.4-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../libpdb-redo_3.0.4-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../libpdb-redo_3.0.4-2_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 2023-01-07T11:01:22Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libpdb-redo_3.0.4-2_armhf.changes:
----------------------------------
Format: 1.8
Date: Fri, 30 Dec 2022 09:12:03 +0100
Source: libpdb-redo
Binary: libpdb-redo-dev libpdb-redo3 libpdb-redo3-dbgsym
Architecture: armhf
Version: 3.0.4-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Maarten L. Hekkelman <maarten@hekkelman.com>
Description:
libpdb-redo-dev - Development files for libpdb-redo
libpdb-redo3 - Library file for libpdb-redo
Changes:
libpdb-redo (3.0.4-2) unstable; urgency=medium
.
* Into unstable.
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Files:
a1bb66b22551dab34ce681929e6eb9ea 628324 libdevel optional libpdb-redo-dev_3.0.4-2_armhf.deb
3e070d632116d51056c4400321211b82 7174692 debug optional libpdb-redo3-dbgsym_3.0.4-2_armhf.deb
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libpdb-redo-dev_3.0.4-2_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 628324 bytes: control archive=1420 bytes.
627 bytes, 16 lines control
1903 bytes, 24 lines md5sums
Package: libpdb-redo-dev
Source: libpdb-redo
Version: 3.0.4-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1071
Depends: libpdb-redo3 (= 3.0.4-2), libboost-regex-dev, libnewuoa-dev, libclipper-dev, zlib1g-dev, libgsl-dev, libcifpp-dev
Section: libdevel
Priority: optional
Homepage: https://github.com/PDB-REDO/libpdb-redo
Description: Development files for libpdb-redo
This library contains shared code for the various programs
in the project PDB-REDO.
.
This specific package contains all files needed to develop new
software using libpdb-redo.
drwxr-xr-x root/root 0 2022-12-30 08:12 ./
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/include/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/include/pdb-redo/
-rw-r--r-- root/root 2344 2022-11-23 13:04 ./usr/include/pdb-redo/AtomShape.hpp
-rw-r--r-- root/root 3454 2022-11-23 13:04 ./usr/include/pdb-redo/BondMap.hpp
-rw-r--r-- root/root 2298 2022-11-23 13:04 ./usr/include/pdb-redo/ClipperWrapper.hpp
-rw-r--r-- root/root 9629 2022-11-23 13:04 ./usr/include/pdb-redo/Compound.hpp
-rw-r--r-- root/root 3072 2022-11-23 13:04 ./usr/include/pdb-redo/DistanceMap.hpp
-rw-r--r-- root/root 6204 2022-11-23 13:04 ./usr/include/pdb-redo/MapMaker.hpp
-rw-r--r-- root/root 5803 2022-11-23 13:04 ./usr/include/pdb-redo/Minimizer.hpp
-rw-r--r-- root/root 1814 2022-11-23 13:04 ./usr/include/pdb-redo/Ramachandran.hpp
-rw-r--r-- root/root 2043 2022-11-23 13:04 ./usr/include/pdb-redo/ResolutionCalculator.hpp
-rw-r--r-- root/root 5990 2022-11-23 13:04 ./usr/include/pdb-redo/Restraints.hpp
-rw-r--r-- root/root 4554 2022-11-23 13:04 ./usr/include/pdb-redo/SkipList.hpp
-rw-r--r-- root/root 5344 2022-11-23 13:04 ./usr/include/pdb-redo/Statistics.hpp
-rw-r--r-- root/root 6271 2022-11-23 13:04 ./usr/include/pdb-redo/Symmetry-2.hpp
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/cmake/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/
-rw-r--r-- root/root 1773 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfig.cmake
-rw-r--r-- root/root 1977 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfigVersion.cmake
-rw-r--r-- root/root 901 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets-none.cmake
-rw-r--r-- root/root 4908 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets.cmake
lrwxrwxrwx root/root 0 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/libpdb-redo.so -> libpdb-redo.so.3
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 303 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/pkgconfig/libpdb-redo.pc
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/doc/libpdb-redo-dev/
-rw-r--r-- root/root 744 2022-12-30 08:12 ./usr/share/doc/libpdb-redo-dev/changelog.Debian.gz
-rw-r--r-- root/root 488 2022-11-23 13:04 ./usr/share/doc/libpdb-redo-dev/changelog.gz
-rw-r--r-- root/root 3497 2022-12-30 08:12 ./usr/share/doc/libpdb-redo-dev/copyright
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/doc/libpdb-redo-dev/examples/
-rw-r--r-- root/root 993520 2022-11-23 13:04 ./usr/share/doc/libpdb-redo-dev/examples/1cbs_map.mtz
-rw-r--r-- root/root 2356 2022-12-30 08:12 ./usr/share/doc/libpdb-redo-dev/examples/CMakeLists.txt
-rw-r--r-- root/root 994 2022-12-30 08:12 ./usr/share/doc/libpdb-redo-dev/examples/example.cpp
libpdb-redo3-dbgsym_3.0.4-2_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 7174692 bytes: control archive=544 bytes.
390 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: libpdb-redo3-dbgsym
Source: libpdb-redo
Version: 3.0.4-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7201
Depends: libpdb-redo3 (= 3.0.4-2)
Section: debug
Priority: optional
Description: debug symbols for libpdb-redo3
Build-Ids: 9c513e2affe85fe52a2c3deb2b972b15dc0b5df6
drwxr-xr-x root/root 0 2022-12-30 08:12 ./
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 7362584 2022-12-30 08:12 ./usr/lib/debug/.build-id/9c/513e2affe85fe52a2c3deb2b972b15dc0b5df6.debug
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-12-30 08:12 ./usr/share/doc/libpdb-redo3-dbgsym -> libpdb-redo3
libpdb-redo3_3.0.4-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 271880 bytes: control archive=884 bytes.
640 bytes, 15 lines control
309 bytes, 4 lines md5sums
38 bytes, 1 lines shlibs
68 bytes, 2 lines triggers
Package: libpdb-redo3
Source: libpdb-redo
Version: 3.0.4-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 851
Depends: libc6 (>= 2.34), libcifpp5 (>= 5.0.5), libclipper2 (>= 2.1.20201109), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libnewuoa0 (>= 0.1.2), libstdc++6 (>= 11), zlib1g (>= 1:1.2.2)
Section: libs
Priority: optional
Homepage: https://github.com/PDB-REDO/libpdb-redo
Description: Library file for libpdb-redo
This library contains shared code for the various programs
in the project PDB-REDO.
.
This package contains the shared library for libpdb-redo.
drwxr-xr-x root/root 0 2022-12-30 08:12 ./
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3 -> libpdb-redo.so.3.0.4
-rw-r--r-- root/root 853920 2022-12-30 08:12 ./usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3.0.4
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-12-30 08:12 ./usr/share/doc/libpdb-redo3/
-rw-r--r-- root/root 744 2022-12-30 08:12 ./usr/share/doc/libpdb-redo3/changelog.Debian.gz
-rw-r--r-- root/root 488 2022-11-23 13:04 ./usr/share/doc/libpdb-redo3/changelog.gz
-rw-r--r-- root/root 3497 2022-12-30 08:12 ./usr/share/doc/libpdb-redo3/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 102164
Build-Time: 551
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 749
Job: libpdb-redo_3.0.4-2
Machine Architecture: armhf
Package: libpdb-redo
Package-Time: 1358
Source-Version: 3.0.4-2
Space: 102164
Status: successful
Version: 3.0.4-2
--------------------------------------------------------------------------------
Finished at 2023-01-07T11:01:22Z
Build needed 00:22:38, 102164k disc space