diamond-aligner →
0.9.30-3 →
armhf → 2020-02-22 05:25:17
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| diamond-aligner 0.9.30-3 (armhf) Sat, 22 Feb 2020 05:18:34 +0000 |
+==============================================================================+
Package: diamond-aligner
Version: 0.9.30-3
Source Version: 0.9.30-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-a712db6c-9a14-4333-99b9-92a4665d85e9' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 10s (2418 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'diamond-aligner' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/diamond-aligner.git
Please use:
git clone https://salsa.debian.org/med-team/diamond-aligner.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 794 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main diamond-aligner 0.9.30-3 (dsc) [2016 B]
Get:2 http://172.17.0.1/private bullseye-staging/main diamond-aligner 0.9.30-3 (tar) [782 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main diamond-aligner 0.9.30-3 (diff) [9924 B]
Fetched 794 kB in 1s (536 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/diamond-aligner-NPaOJk/diamond-aligner-0.9.30' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/diamond-aligner-NPaOJk' 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-sGa7Ea/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-sGa7Ea/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-sGa7Ea/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-sGa7Ea/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Packages [429 B]
Fetched 2105 B in 0s (9999 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 26 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-sGa7Ea/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12214 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 (= 12), cmake, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 12), cmake, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-diamond-aligner-dummy' in '/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive/sbuild-build-depends-diamond-aligner-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-diamond-aligner-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-sGa7Ea/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Sources [508 B]
Get:5 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ Packages [589 B]
Fetched 2430 B in 0s (11.5 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install diamond-aligner build dependencies (apt-based resolver)
---------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13
libbrotli1 libbsd0 libcroco3 libcurl4 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libicu63
libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libprocps7 libpsl5
librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl
libtinfo5 libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps
sensible-utils zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff lrzip krb5-doc krb5-user libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13
libbrotli1 libbsd0 libcroco3 libcurl4 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libicu63
libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc
libmagic1 libncurses6 libnghttp2-14 libpipeline1 libprocps7 libpsl5
librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl
libtinfo5 libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps
sbuild-build-depends-diamond-aligner-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
zlib1g
1 upgraded, 59 newly installed, 0 to remove and 25 not upgraded.
Need to get 27.0 MB of archives.
After this operation, 101 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-sGa7Ea/apt_archive ./ sbuild-build-depends-diamond-aligner-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-1.2 [84.6 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libprocps7 armhf 2:3.3.15-2 [58.9 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.15-2 [235 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.16.3-1 [1628 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.0-1+b1 [292 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.67.0-2 [286 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.9-1 [133 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.34.2-1 [114 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.16.3-1 [2648 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-13 [513 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.9 [183 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-2 [1138 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.9 [994 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1.2 [203 kB]
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Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-4) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libuv1:armhf (1.34.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1.2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up librhash0:armhf (1.3.9-1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up procps (2:3.3.15-2) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up cmake-data (3.16.3-1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libjsoncpp1:armhf (1.7.4-3.1) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up libtool (2.4.6-13) ...
Setting up libarchive13:armhf (3.4.0-1+b1) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libcurl4:armhf (7.67.0-2) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up cmake (3.16.3-1) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.9) ...
Setting up sbuild-build-depends-diamond-aligner-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-9+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.90.20200122-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-9+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.90.20200122-2+rpi1 binutils-arm-linux-gnueabihf_2.33.90.20200122-2+rpi1 binutils-common_2.33.90.20200122-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 cmake_3.16.3-1 cmake-data_3.16.3-1 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-25+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libarchive13_3.4.0-1+b1 libasan5_9.2.1-25+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.90.20200122-2+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-9+rpi1 libc-dev-bin_2.29-9+rpi1 libc6_2.29-9+rpi1 libc6-dev_2.29-9+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-25+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libctf-nobfd0_2.33.90.20200122-2+rpi1 libctf0_2.33.90.20200122-2+rpi1 libcurl4_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.9 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.2.1-25+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2+b1 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libreadline7_7.0-5 libreadline8_8.0-3 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.0+really3.30.1+fossil191229-1 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.1-1+rpi1 libtasn1-6_4.15.0-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libubsan1_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.1-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.34.2-1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-1 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-diamond-aligner-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1.2 zlib1g-dev_1:1.2.11.dfsg-1.2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Feb 17 13:23:03 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./diamond-aligner_0.9.30-3.dsc
dpkg-source: info: extracting diamond-aligner in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking diamond-aligner_0.9.30.orig.tar.xz
dpkg-source: info: unpacking diamond-aligner_0.9.30-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying avoid_unwanted_optimisation.patch
dpkg-source: info: applying 82feea2aee5c82e283704b9317cb5e8abc625f90.patch
dpkg-source: info: applying multi_arch
dpkg-source: info: applying fix_i386_and_s390x
Check disk 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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-a712db6c-9a14-4333-99b9-92a4665d85e9
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package diamond-aligner
dpkg-buildpackage: info: source version 0.9.30-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DX86=OFF
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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DX86=OFF ..
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
-- 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"
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/arch_generic.dir/build.make CMakeFiles/arch_generic.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/arch_generic.dir/DependInfo.cmake --color=
Scanning dependencies of target arch_generic
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 24%] Building CXX object CMakeFiles/diamond.dir/src/data/seed_histogram.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/seed_histogram.cpp.o -c /<<PKGBUILDDIR>>/src/data/seed_histogram.cpp
[ 25%] Building CXX object CMakeFiles/diamond.dir/src/output/daa_record.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/daa_record.cpp.o -c /<<PKGBUILDDIR>>/src/output/daa_record.cpp
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/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/command_line_parser.cpp.o -c /<<PKGBUILDDIR>>/src/util/command_line_parser.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/data/../basic/config.h:23,
from /<<PKGBUILDDIR>>/src/data/reference.cpp:24:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int&, unsigned int}; _Tp = Pos_record; _Alloc = std::allocator<Pos_record>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Pos_record>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<Pos_record*, std::vector<Pos_record> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function ‘void push_seq(const sequence&, const sequence&, uint64_t&, std::vector<Pos_record>&, OutputFile&, size_t&, size_t&)’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Pos_record*, std::vector<Pos_record> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int&, int}; _Tp = Pos_record; _Alloc = std::allocator<Pos_record>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Pos_record>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<Pos_record*, std::vector<Pos_record> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function ‘bool DatabaseFile::load_seqs(std::vector<unsigned int>&, size_t, Sequence_set**, String_set<'\000'>**, bool, const std::vector<bool>*)’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
[ 26%] Building CXX object CMakeFiles/diamond.dir/src/util/seq_file_format.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/seq_file_format.cpp.o -c /<<PKGBUILDDIR>>/src/util/seq_file_format.cpp
/<<PKGBUILDDIR>>/src/data/reference.cpp:339:1: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’} changed in GCC 7.1
339 | }
| ^
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/data/../basic/config.h:23,
from /<<PKGBUILDDIR>>/src/data/reference.cpp:24:
/usr/include/c++/9/bits/vector.tcc: In function ‘void make_db(TempFile**, TextInputFile*)’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Pos_record*, std::vector<Pos_record> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/data/reference.cpp:256:1: note: parameter passing for argument of type ‘std::vector<Pos_record>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<Pos_record*, std::vector<Pos_record> >’} changed in GCC 7.1
256 | }
| ^
[ 27%] Building CXX object CMakeFiles/diamond.dir/src/util/util.cpp.o
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[ 28%] Building CXX object CMakeFiles/diamond.dir/src/basic/basic.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/basic/basic.cpp.o -c /<<PKGBUILDDIR>>/src/basic/basic.cpp
[ 29%] Building CXX object CMakeFiles/diamond.dir/src/basic/hssp.cpp.o
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53 | target_parallel = (end - begin > config.query_parallel_limit) && ((config.frame_shift != 0 && align_mode.mode == Align_mode::blastx && config.toppercent < 100 && config.query_range_culling)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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105 | if (sscanf(f.line.c_str(), "%u\t|\t%u\t|\t%63[^\t]", &taxid, &parent, &rank) != 3)
| ~~~~~^~ ~~~~~
| | |
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/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/taxonomy_nodes.cpp.o -c /<<PKGBUILDDIR>>/src/data/taxonomy_nodes.cpp
[ 72%] Building CXX object CMakeFiles/diamond.dir/src/util/algo/MurmurHash3.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/algo/MurmurHash3.cpp.o -c /<<PKGBUILDDIR>>/src/util/algo/MurmurHash3.cpp
[ 73%] Building CXX object CMakeFiles/diamond.dir/src/search/stage0.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/search/stage0.cpp.o -c /<<PKGBUILDDIR>>/src/search/stage0.cpp
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[ 75%] Building CXX object CMakeFiles/diamond.dir/src/output/paf_format.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/paf_format.cpp.o -c /<<PKGBUILDDIR>>/src/output/paf_format.cpp
[ 75%] Building CXX object CMakeFiles/diamond.dir/src/util/system/system.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/system/system.cpp.o -c /<<PKGBUILDDIR>>/src/util/system/system.cpp
[ 76%] Building CXX object CMakeFiles/diamond.dir/src/run/cluster.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/run/cluster.cpp.o -c /<<PKGBUILDDIR>>/src/run/cluster.cpp
[ 77%] Building CXX object CMakeFiles/diamond.dir/src/util/algo/greedy_vortex_cover.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/algo/greedy_vortex_cover.cpp.o -c /<<PKGBUILDDIR>>/src/util/algo/greedy_vortex_cover.cpp
[ 78%] Building CXX object CMakeFiles/diamond.dir/src/util/sequence/sequence.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/sequence/sequence.cpp.o -c /<<PKGBUILDDIR>>/src/util/sequence/sequence.cpp
[ 79%] Building CXX object CMakeFiles/diamond.dir/src/tools/tsv_record.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/tools/tsv_record.cpp.o -c /<<PKGBUILDDIR>>/src/tools/tsv_record.cpp
[ 80%] Building CXX object CMakeFiles/diamond.dir/src/tools/tools.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/tools/tools.cpp.o -c /<<PKGBUILDDIR>>/src/tools/tools.cpp
[ 81%] Building CXX object CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/system/getRSS.cpp.o -c /<<PKGBUILDDIR>>/src/util/system/getRSS.cpp
[ 82%] Building CXX object CMakeFiles/diamond.dir/src/util/math/sparse_matrix.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/math/sparse_matrix.cpp.o -c /<<PKGBUILDDIR>>/src/util/math/sparse_matrix.cpp
[ 83%] Building CXX object CMakeFiles/diamond.dir/src/lib/tantan/LambdaCalculator.cc.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/lib/tantan/LambdaCalculator.cc.o -c /<<PKGBUILDDIR>>/src/lib/tantan/LambdaCalculator.cc
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/lib/tantan/LambdaCalculator.hh:16,
from /<<PKGBUILDDIR>>/src/lib/tantan/LambdaCalculator.cc:3:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
[ 84%] Building CXX object CMakeFiles/diamond.dir/src/data/taxonomy_filter.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/data/taxonomy_filter.cpp.o -c /<<PKGBUILDDIR>>/src/data/taxonomy_filter.cpp
[ 85%] Building CXX object CMakeFiles/diamond.dir/src/util/algo/upgma.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/algo/upgma.cpp.o -c /<<PKGBUILDDIR>>/src/util/algo/upgma.cpp
[ 86%] Building CXX object CMakeFiles/diamond.dir/src/util/algo/upgma_mc.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/algo/upgma_mc.cpp.o -c /<<PKGBUILDDIR>>/src/util/algo/upgma_mc.cpp
In file included from /usr/include/c++/9/queue:62,
from /<<PKGBUILDDIR>>/src/util/algo/upgma.cpp:4:
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA::Edge> > >; _Distance = int; _Tp = std::_List_iterator<Util::Algo::UPGMA::Edge>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<Util::Algo::UPGMA::CmpEdge>]’:
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’ changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA::Edge> > >; _Distance = int; _Tp = std::_List_iterator<Util::Algo::UPGMA::Edge>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<Util::Algo::UPGMA::CmpEdge>]’:
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’ changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:237:23: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’ changed in GCC 7.1
237 | std::__push_heap(__first, __holeIndex, __topIndex,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
238 | _GLIBCXX_MOVE(__value), __cmp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 87%] Building CXX object CMakeFiles/diamond.dir/src/util/algo/edge_vec.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/algo/edge_vec.cpp.o -c /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp
/usr/include/c++/9/bits/stl_heap.h: In function ‘void Util::Algo::UPGMA::merge_nodes(int, int, std::vector<Util::Algo::UPGMA::Node>&, Util::Algo::UPGMA::EdgeList&, Util::Algo::UPGMA::Queue&, double)’:
/usr/include/c++/9/bits/stl_heap.h:207:23: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’} changed in GCC 7.1
207 | std::__push_heap(__first, _DistanceType((__last - __first) - 1),
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
208 | _DistanceType(0), _GLIBCXX_MOVE(__value), __cmp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA::Edge> > >; _Distance = int; _Tp = std::_List_iterator<Util::Algo::UPGMA::Edge>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<Util::Algo::UPGMA::Node::CmpNeighbor>]’:
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’ changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA::Edge> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<Util::Algo::UPGMA::Node::CmpNeighbor>]’:
/usr/include/c++/9/bits/stl_heap.h:342:22: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’} changed in GCC 7.1
342 | std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
343 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:253:25: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’} changed in GCC 7.1
253 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 88%] Building CXX object CMakeFiles/diamond.dir/src/util/string/string.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/string/string.cpp.o -c /<<PKGBUILDDIR>>/src/util/string/string.cpp
/usr/include/c++/9/bits/stl_heap.h: In function ‘void Util::Algo::UPGMA::upgma(Util::Algo::UPGMA::EdgeList&, size_t)’:
/usr/include/c++/9/bits/stl_heap.h:342:22: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’} changed in GCC 7.1
342 | std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
343 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:253:25: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA::Edge>’} changed in GCC 7.1
253 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 89%] Building CXX object CMakeFiles/diamond.dir/src/align/extend.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/align/extend.cpp.o -c /<<PKGBUILDDIR>>/src/align/extend.cpp
In file included from /usr/include/c++/9/queue:62,
from /<<PKGBUILDDIR>>/src/util/algo/upgma_mc.cpp:4:
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA_MC::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA_MC::Edge> > >; _Distance = int; _Tp = std::_List_iterator<Util::Algo::UPGMA_MC::Edge>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<Util::Algo::UPGMA_MC::CmpEdge>]’:
/usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’ changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA_MC::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA_MC::Edge> > >; _Distance = int; _Tp = std::_List_iterator<Util::Algo::UPGMA_MC::Edge>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<Util::Algo::UPGMA_MC::CmpEdge>]’:
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’ changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:237:23: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’ changed in GCC 7.1
237 | std::__push_heap(__first, __holeIndex, __topIndex,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
238 | _GLIBCXX_MOVE(__value), __cmp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void Util::Algo::UPGMA_MC::merge_nodes(int, int, std::vector<Util::Algo::UPGMA_MC::Node>&, Util::Algo::UPGMA_MC::EdgeList&, Util::Algo::UPGMA_MC::Queue&, double, double)’:
/usr/include/c++/9/bits/stl_heap.h:207:23: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’} changed in GCC 7.1
207 | std::__push_heap(__first, _DistanceType((__last - __first) - 1),
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
208 | _DistanceType(0), _GLIBCXX_MOVE(__value), __cmp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/tuple:41,
from /usr/include/c++/9/bits/hashtable_policy.h:34,
from /usr/include/c++/9/bits/hashtable.h:35,
from /usr/include/c++/9/unordered_map:46,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.h:4,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:5:
/usr/include/c++/9/bits/invoke.h: In member function ‘void std::thread::_State_impl<_Callable>::_M_run() [with _Callable = std::thread::_Invoker<std::tuple<void (*)(__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge, std::allocator<Util::Algo::UPGMA_MC::CompactEdge> > >, __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge, std::allocator<Util::Algo::UPGMA_MC::CompactEdge> > >, unsigned int, unsigned int), __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge, std::allocator<Util::Algo::UPGMA_MC::CompactEdge> > >, __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge, std::allocator<Util::Algo::UPGMA_MC::CompactEdge> > >, unsigned int, unsigned int> >]’:
/usr/include/c++/9/bits/invoke.h:60:36: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
60 | { return std::forward<_Fn>(__f)(std::forward<_Args>(__args)...); }
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA_MC::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA_MC::Edge> > >; _Distance = int; _Tp = std::_List_iterator<Util::Algo::UPGMA_MC::Edge>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<Util::Algo::UPGMA_MC::Node::CmpNeighbor>]’:
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’ changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::_List_iterator<Util::Algo::UPGMA_MC::Edge>*, std::vector<std::_List_iterator<Util::Algo::UPGMA_MC::Edge> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<Util::Algo::UPGMA_MC::Node::CmpNeighbor>]’:
/usr/include/c++/9/bits/stl_heap.h:342:22: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’} changed in GCC 7.1
342 | std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
343 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:253:25: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’} changed in GCC 7.1
253 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.h:9,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:5:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Util::Algo::UPGMA_MC::CompactEdge}; _Tp = Util::Algo::UPGMA_MC::CompactEdge; _Alloc = std::allocator<Util::Algo::UPGMA_MC::CompactEdge>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Util::Algo::UPGMA_MC::CompactEdge>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Util::Algo::UPGMA_MC::CompactEdge}; _Tp = Util::Algo::UPGMA_MC::CompactEdge; _Alloc = std::allocator<Util::Algo::UPGMA_MC::CompactEdge>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘double Util::Algo::UPGMA_MC::load_edges(Util::Algo::UPGMA_MC::EdgeVec&, Util::Algo::UPGMA_MC::EdgeList&, std::vector<Util::Algo::UPGMA_MC::Node>&, Util::Algo::UPGMA_MC::Queue&, double, double)’:
/usr/include/c++/9/bits/stl_heap.h:342:22: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’} changed in GCC 7.1
342 | std::__adjust_heap(__first, __parent, __len, _GLIBCXX_MOVE(__value),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
343 | __comp);
| ~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:4:
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
[ 90%] Building CXX object CMakeFiles/diamond.dir/src/align/target.cpp.o
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/bin/c++ -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/lib -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable -std=gnu++11 -o CMakeFiles/diamond.dir/src/align/target.cpp.o -c /<<PKGBUILDDIR>>/src/align/target.cpp
/usr/include/c++/9/bits/stl_algo.h: In function ‘_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >]’:
/usr/include/c++/9/bits/stl_algo.h:1328:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1328 | __rotate(_RandomAccessIterator __first,
| ^~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1328:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1328:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/9/bits/stl_algo.h:2471:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2471 | __merge_without_buffer(_BidirectionalIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2471:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:2471:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1443:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1443 | return std::__rotate(__first, __middle, __last,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1444 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2512:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2512 | std::__merge_without_buffer(__first, __first_cut, __new_middle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2513 | __len11, __len22, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2514:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2514 | std::__merge_without_buffer(__new_middle, __second_cut, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2515 | __len1 - __len11, __len2 - __len22, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >; _Distance = int; _Pointer = Util::Algo::UPGMA_MC::CompactEdge*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/9/bits/stl_algo.h:2410:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2410 | __merge_adaptive(_BidirectionalIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2410:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:2410:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1443:27: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1443 | return std::__rotate(__first, __middle, __last,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1444 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2458:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2458 | std::__merge_adaptive(__first, __first_cut, __new_middle, __len11,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2459 | __len22, __buffer, __buffer_size, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2460:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2460 | std::__merge_adaptive(__new_middle, __second_cut, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2461 | __len1 - __len11,
| ~~~~~~~~~~~~~~~~~
2462 | __len2 - __len22, __buffer,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2463 | __buffer_size, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:4:
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >; _Distance = int; _Tp = Util::Algo::UPGMA_MC::CompactEdge; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:4:
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:8:
/<<PKGBUILDDIR>>/src/util/algo/../merge_sort.h: In function ‘void merge_sort(_it, _it, unsigned int, unsigned int) [with _it = __gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >]’:
/<<PKGBUILDDIR>>/src/util/algo/../merge_sort.h:27:6: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
27 | void merge_sort(_it begin, _it end, unsigned n_threads, unsigned level = 0)
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/util/algo/../merge_sort.h:27:6: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:4:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2541:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2540 | std::__merge_without_buffer
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2541 | (__first, __middle, __last, __len1, __len2, __comp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:2544:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
2543 | std::__merge_adaptive
| ~~~~~~~~~~~~~~~~~~~~~
2544 | (__first, __middle, __last, __len1, __len2, __buf.begin(),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2545 | _DistanceType(__buf.size()), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp: In member function ‘Util::Algo::UPGMA_MC::CompactEdge Util::Algo::UPGMA_MC::EdgeVec::get()’:
/<<PKGBUILDDIR>>/src/util/algo/edge_vec.cpp:109:13: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Util::Algo::UPGMA_MC::CompactEdge*, std::vector<Util::Algo::UPGMA_MC::CompactEdge> >’ changed in GCC 7.1
109 | merge_sort(buffer_.begin(), buffer_.end(), config.threads_);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function ‘void Util::Algo::UPGMA_MC::upgma()’:
/usr/include/c++/9/bits/stl_heap.h:253:25: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’} changed in GCC 7.1
253 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:253:25: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’} changed in GCC 7.1
253 | std::__adjust_heap(__first, _DistanceType(0),
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | _DistanceType(__last - __first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
255 | _GLIBCXX_MOVE(__value), __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:207:23: note: parameter passing for argument of type ‘_ValueType’ {aka ‘std::_List_iterator<Util::Algo::UPGMA_MC::Edge>’} changed in GCC 7.1
207 | std::__push_heap(__first, _DistanceType((__last - __first) - 1),
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
208 | _DistanceType(0), _GLIBCXX_MOVE(__value), __cmp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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dpkg-genbuildinfo --build=any
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dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-02-22T05:25:10Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
diamond-aligner_0.9.30-3_armhf.changes:
---------------------------------------
Format: 1.8
Date: Mon, 17 Feb 2020 14:22:48 +0100
Source: diamond-aligner
Binary: diamond-aligner diamond-aligner-dbgsym
Architecture: armhf
Version: 0.9.30-3
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
diamond-aligner - accelerated BLAST compatible local sequence aligner
Changes:
diamond-aligner (0.9.30-3) unstable; urgency=medium
.
* Team upload.
* Patch from upstream to fix i386 & s390x builds
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Files:
2b70bb9c1ab506962fe9ace1984038d7 8514112 debug optional diamond-aligner-dbgsym_0.9.30-3_armhf.deb
b1193999e56b0e754c0b5a7689f13aa7 5800 science optional diamond-aligner_0.9.30-3_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
diamond-aligner-dbgsym_0.9.30-3_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 8514112 bytes: control archive=540 bytes.
405 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: diamond-aligner-dbgsym
Source: diamond-aligner
Version: 0.9.30-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8566
Depends: diamond-aligner (= 0.9.30-3)
Section: debug
Priority: optional
Description: debug symbols for diamond-aligner
Build-Ids: 347174f10a7835f9a2bc69ebe22f39eb6d3064a1
drwxr-xr-x root/root 0 2020-02-17 13:22 ./
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/lib/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 8760336 2020-02-17 13:22 ./usr/lib/debug/.build-id/34/7174f10a7835f9a2bc69ebe22f39eb6d3064a1.debug
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/share/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-02-17 13:22 ./usr/share/doc/diamond-aligner-dbgsym -> diamond-aligner
diamond-aligner_0.9.30-3_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 475328 bytes: control archive=924 bytes.
811 bytes, 18 lines control
348 bytes, 5 lines md5sums
Package: diamond-aligner
Version: 0.9.30-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1309
Depends: libc6 (>= 2.29), libgcc1 (>= 1:3.5), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: med-config (>= 2.1)
Breaks: diamond
Replaces: diamond
Section: science
Priority: optional
Homepage: https://github.com/bbuchfink/diamond
Description: accelerated BLAST compatible local sequence aligner
DIAMOND is a sequence aligner for protein and translated DNA searches
and functions as a drop-in replacement for the NCBI BLAST software
tools. It is suitable for protein-protein search as well as DNA-protein
search on short reads and longer sequences including contigs and
assemblies, providing a speedup of BLAST ranging up to x20,000.
drwxr-xr-x root/root 0 2020-02-17 13:22 ./
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/bin/
-rwxr-xr-x root/root 1320400 2020-02-17 13:22 ./usr/bin/diamond
lrwxrwxrwx root/root 0 2020-02-17 13:22 ./usr/bin/diamond-aligner -> diamond
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/share/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/share/doc/diamond-aligner/
-rw-r--r-- root/root 91 2020-02-02 17:27 ./usr/share/doc/diamond-aligner/README.md
-rw-r--r-- root/root 1272 2020-02-17 13:22 ./usr/share/doc/diamond-aligner/changelog.Debian.gz
-rw-r--r-- root/root 1307 2020-02-06 15:09 ./usr/share/doc/diamond-aligner/copyright
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/share/man/
drwxr-xr-x root/root 0 2020-02-17 13:22 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2020-02-17 13:22 ./usr/share/man/man1/diamond-aligner.1.gz -> diamond.1.gz
-rw-r--r-- root/root 2421 2020-02-17 13:22 ./usr/share/man/man1/diamond.1.gz
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Build Architecture: armhf
Build-Space: 129828
Build-Time: 170
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 208
Job: diamond-aligner_0.9.30-3
Machine Architecture: armhf
Package: diamond-aligner
Package-Time: 396
Source-Version: 0.9.30-3
Space: 129828
Status: successful
Version: 0.9.30-3
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Finished at 2020-02-22T05:25:10Z
Build needed 00:06:36, 129828k disk space