ngmlr →
0.2.7+dfsg-4 →
armhf → 2020-12-14 08:40:33
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| ngmlr 0.2.7+dfsg-4 (armhf) Mon, 14 Dec 2020 08:28:58 +0000 |
+==============================================================================+
Package: ngmlr
Version: 0.2.7+dfsg-4
Source Version: 0.2.7+dfsg-4
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-e6551930-99fd-4f5f-bb4a-67dfaef759e9' 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 [12.0 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.9 MB in 25s (1016 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: 'ngmlr' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/ngmlr.git
Please use:
git clone https://salsa.debian.org/med-team/ngmlr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 676 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main ngmlr 0.2.7+dfsg-4 (dsc) [2119 B]
Get:2 http://172.17.0.1/private bullseye-staging/main ngmlr 0.2.7+dfsg-4 (tar) [668 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main ngmlr 0.2.7+dfsg-4 (diff) [6468 B]
Fetched 676 kB in 0s (3679 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/ngmlr-jeoicx/ngmlr-0.2.7+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ngmlr-jeoicx' 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-rR7kzj/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-rR7kzj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-rR7kzj/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-rR7kzj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2756 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:
bsdextrautils krb5-locales libnss-nis libnss-nisplus 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 5 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (13.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12776 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), cmake, zlib1g-dev, libssw-dev, libtclap-dev, libhts-dev, libsimde-dev
Filtered Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libssw-dev, libtclap-dev, libhts-dev, libsimde-dev
dpkg-deb: building package 'sbuild-build-depends-ngmlr-dummy' in '/<<BUILDDIR>>/resolver-rR7kzj/apt_archive/sbuild-build-depends-ngmlr-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-ngmlr-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-rR7kzj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Sources [526 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ Packages [604 B]
Fetched 2463 B in 1s (3277 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install ngmlr 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 libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libarchive13 libbrotli1
libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts3 libicu67
libjsoncpp24 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14
libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2 libsimde-dev
libssh2-1 libssw-dev libssw0 libsub-override-perl libtclap-dev libtool
libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make
gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libcurl4-doc
libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev pkg-config liblzma-doc 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 libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libarchive13 libbrotli1
libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts3 libicu67
libjsoncpp24 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14
libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2 libsimde-dev
libssh2-1 libssw-dev libssw0 libsub-override-perl libtclap-dev libtool
libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps
sbuild-build-depends-ngmlr-dummy zlib1g-dev
0 upgraded, 60 newly installed, 0 to remove and 5 not upgraded.
Need to get 31.6 MB of archives.
After this operation, 115 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rR7kzj/apt_archive ./ sbuild-build-depends-ngmlr-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-1 [79.5 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.18.4-1+rpi1 [1725 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-5 [8288 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-1 [141 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.72.0-1 [300 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp24 armhf 1.9.4-3 [66.9 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.0-1 [133 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.40.0-1 [118 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.18.4-1+rpi1+b1 [3111 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3 [188 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20201015-2 [162 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-2 [1178 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3 [1009 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.72.0-1 [297 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.72.0-1 [371 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libsimde-dev all 0.6.0-3 [213 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libssw0 armhf 1.1-11 [20.4 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libssw-dev armhf 1.1-11 [23.8 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libtclap-dev armhf 1.2.2-1 [139 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:armhf (2.2.10-1) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libsimde-dev (0.6.0-3) ...
Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up libicu67:armhf (67.1-5) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.3-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.3) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.42.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.6-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libuv1:armhf (1.40.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libtclap-dev (1.2.2-1) ...
Setting up libjsoncpp24:armhf (1.9.4-3) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up librhash0:armhf (1.4.0-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-1) ...
Setting up cmake-data (3.18.4-1+rpi1) ...
Setting up libdeflate-dev:armhf (1.6-1) ...
Setting up libelf1:armhf (0.182-1) ...
Setting up libssw0:armhf (1.1-11) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libprocps8:armhf (2:3.3.16-5) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libssw-dev:armhf (1.1-11) ...
Setting up libtool (2.4.6-14) ...
Setting up libarchive13:armhf (3.4.3-2) ...
Setting up m4 (1.4.18-4) ...
Setting up libcurl3-gnutls:armhf (7.72.0-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.72.0-1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13+20201015-2) ...
Setting up groff-base (1.22.4-5) ...
Setting up procps (2:3.3.16-5) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libcurl4:armhf (7.72.0-1) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.11-2) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libhts-dev:armhf (1.11-2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up cmake (3.18.4-1+rpi1+b1) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13.3) ...
Setting up sbuild-build-depends-ngmlr-dummy (0.invalid.0) ...
Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.31-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-4+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-19+rpi1 gcc-10_10.2.0-19+rpi1 libc6-dev_2.31-5+rpi1 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1
Package versions: adduser_3.118 apt_2.1.12 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc3-1 binutils_2.35.1-4+rpi1 binutils-arm-linux-gnueabihf_2.35.1-4+rpi1 binutils-common_2.35.1-4+rpi1 bsdextrautils_2.36.1-2 bsdutils_1:2.36.1-2 build-essential_12.8 bzip2_1.0.8-4 cmake_3.18.4-1+rpi1+b1 cmake-data_3.18.4-1+rpi1 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-19+rpi1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.3 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-2 file_1:5.39-3 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-19+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-19+rpi1 gcc-10-base_10.2.0-19+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.59 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.18.3-4 libacl1_2.2.53-8 libapt-pkg6.0_2.1.12 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.0-19+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-19+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1+b1 libbinutils_2.35.1-4+rpi1 libblkid1_2.36.1-2 libboost-iostreams1.71.0_1.71.0-7+b1 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-5+rpi1 libc-dev-bin_2.31-5+rpi1 libc6_2.31-5+rpi1 libc6-dev_2.31-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-19+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-4+rpi1 libctf0_2.35.1-4+rpi1 libcurl3-gnutls_7.72.0-1 libcurl4_7.72.0-1 libcurl4-gnutls-dev_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255 libdebhelper-perl_13.3 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-2 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-19+rpi1 libgcc-s1_10.2.0-19+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.3-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.6.15-4 libgomp1_10.2.0-19+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu67_67.1-5 libidn2-0_2.3.0-4 libisl23_0.23-1 libjsoncpp24_1.9.4-3 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-1 libncursesw6_6.2+20201114-1 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.35-2 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libreadline8_8.1~rc3-1 librhash0_1.4.0-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsimde-dev_0.6.0-3 libsmartcols1_2.36.1-2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1 libssh2-1_1.9.0-1 libssl1.1_1.1.1h-1 libssw-dev_1.1-11 libssw0_1.1-11 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-4+rpi1 libtasn1-6_4.16.0-2 libtclap-dev_1.2.2-1 libtinfo6_6.2+20201114-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-19+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-4+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-2 libuv1_1.40.0-1 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.3 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-2 ncurses-base_6.2+20201114-1 ncurses-bin_6.2+20201114-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ngmlr-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020d-1 util-linux_2.36.1-2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.agjWamtA/trustedkeys.kbx': General error
gpgv: Signature made Sun Dec 6 13:12:41 2020 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./ngmlr_0.2.7+dfsg-4.dsc
dpkg-source: info: extracting ngmlr in /<<BUILDDIR>>/ngmlr-0.2.7+dfsg
dpkg-source: info: unpacking ngmlr_0.2.7+dfsg.orig.tar.gz
dpkg-source: info: unpacking ngmlr_0.2.7+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use-system-libs.patch
dpkg-source: info: applying spellings.patch
dpkg-source: info: applying simde.patch
dpkg-source: info: applying fix-type-incompatibilities.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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-e6551930-99fd-4f5f-bb4a-67dfaef759e9
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package ngmlr
dpkg-buildpackage: info: source version 0.2.7+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem cmake
dh_auto_clean -O--buildsystem=cmake
dh_autoreconf_clean -O--buildsystem=cmake
dh_clean -O--buildsystem=cmake
debian/rules binary-arch
dh binary-arch --buildsystem cmake
dh_update_autotools_config -a -O--buildsystem=cmake
dh_autoreconf -a -O--buildsystem=cmake
dh_auto_configure -a -O--buildsystem=cmake
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 -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ..
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- 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
-- 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
-- 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
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
-- 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: /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf
dh_auto_build -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/ngmlr-0.2.7+dfsg -B/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/recompile_always.dir/build.make src/CMakeFiles/recompile_always.dir/depend
make[3]: Entering directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/ngmlr-0.2.7+dfsg /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/recompile_always.dir/DependInfo.cmake --color=
make -f src/CMakeFiles/ngmlr.dir/build.make src/CMakeFiles/ngmlr.dir/depend
make[3]: Entering directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/ngmlr-0.2.7+dfsg /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/ngmlr.dir/DependInfo.cmake --color=
Dependee "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/recompile_always.dir/DependInfo.cmake" is newer than depender "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/recompile_always.dir/depend.internal".
Dependee "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/recompile_always.dir/depend.internal".
Scanning dependencies of target recompile_always
make[3]: Leaving directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/recompile_always.dir/build.make src/CMakeFiles/recompile_always.dir/build
Dependee "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/ngmlr.dir/DependInfo.cmake" is newer than depender "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/ngmlr.dir/depend.internal".
Dependee "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/ngmlr.dir/depend.internal".
make[3]: Entering directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && touch /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/main.cpp
make[3]: Leaving directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
[ 0%] Built target recompile_always
Scanning dependencies of target ngmlr
make[3]: Leaving directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/ngmlr.dir/build.make src/CMakeFiles/ngmlr.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
[ 4%] Building CXX object src/CMakeFiles/ngmlr.dir/AlignmentMatrix.cpp.o
[ 12%] Building CXX object src/CMakeFiles/ngmlr.dir/ArgParser.cpp.o
[ 12%] Building CXX object src/CMakeFiles/ngmlr.dir/CS.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/AlignmentMatrix.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/AlignmentMatrix.cpp
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/ArgParser.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/ArgParser.cpp
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/CS.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/CS.cpp
[ 16%] Building CXX object src/CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/AlignmentMatrixFast.cpp
[ 20%] Building CXX object src/CMakeFiles/ngmlr.dir/CSstatic.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/CSstatic.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/CSstatic.cpp
[ 24%] Building CXX object src/CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/ConvexAlign.cpp
[ 28%] Building CXX object src/CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/ConvexAlignFast.cpp
[ 32%] Building CXX object src/CMakeFiles/ngmlr.dir/LinearRegression.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/LinearRegression.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/LinearRegression.cpp
[ 36%] Building CXX object src/CMakeFiles/ngmlr.dir/Logging.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/Logging.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Logging.cpp
[ 40%] Building CXX object src/CMakeFiles/ngmlr.dir/MappedRead.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/MappedRead.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/MappedRead.cpp
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Logging.cpp: In function ‘void __Log::LogToConsole(bool, int, const char*, const char*, ...)’:
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Logging.cpp:100:2: warning: second parameter of ‘va_start’ not last named argument [-Wvarargs]
100 | va_start(args, count);
| ^~~~~~~~
[ 44%] Building CXX object src/CMakeFiles/ngmlr.dir/main.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/main.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/main.cpp
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Logging.cpp: In function ‘std::string add_timestamp(std::string)’:
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Logging.cpp:125:27: warning: ‘%02i’ directive writing between 2 and 11 bytes into a region of size between 8 and 15 [-Wformat-overflow=]
125 | sprintf(timestamp, "%4i-%02i-%02i_%02i-%02i-%02i", tm->tm_year + 1900, tm->tm_mon + 1, tm->tm_mday, tm->tm_hour, tm->tm_min,
| ^~~~
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Logging.cpp:125:22: note: directive argument in the range [-2147483647, 2147483647]
125 | sprintf(timestamp, "%4i-%02i-%02i_%02i-%02i-%02i", tm->tm_year + 1900, tm->tm_mon + 1, tm->tm_mday, tm->tm_hour, tm->tm_min,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Logging.cpp:7:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 20 and 72 bytes into a destination of size 20
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/main.cpp:56:146: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
56 | Log.Message("ngmlr %s%s (build: %s %s, start: %s)", version.str().c_str(), cDebug ? " debug" : "", __DATE__, __TIME__, currentDateTime().c_str());
| ^
In file included from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/Log.h:8,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/NGM.h:11,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/main.cpp:5:
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/main.cpp:56:101: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
56 | Log.Message("ngmlr %s%s (build: %s %s, start: %s)", version.str().c_str(), cDebug ? " debug" : "", __DATE__, __TIME__, currentDateTime().c_str());
| ^~~~~~~~
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/ILog.h:44:56: note: in definition of macro ‘Message’
44 | #define Message(s, ...) _Message(0, module_name, s , ##__VA_ARGS__)
| ^~~~~~~~~~~
[ 48%] Building CXX object src/CMakeFiles/ngmlr.dir/NGM.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/NGM.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/NGM.cpp
[ 52%] Building CXX object src/CMakeFiles/ngmlr.dir/NGMTask.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/NGMTask.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/NGMTask.cpp
[ 56%] Building CXX object src/CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/AlignmentBuffer.cpp
[ 60%] Building CXX object src/CMakeFiles/ngmlr.dir/PrefixTable.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/PrefixTable.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/PrefixTable.cpp
[ 64%] Building CXX object src/CMakeFiles/ngmlr.dir/ReadProvider.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/ReadProvider.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/ReadProvider.cpp
[ 68%] Building CXX object src/CMakeFiles/ngmlr.dir/SamParser.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/SamParser.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/SamParser.cpp
[ 72%] Building CXX object src/CMakeFiles/ngmlr.dir/SAMWriter.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/SAMWriter.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/SAMWriter.cpp
[ 76%] Building CXX object src/CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/SequenceProvider.cpp
[ 80%] Building CXX object src/CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/OutputReadBuffer.cpp
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/OutputReadBuffer.cpp: In destructor ‘OutputReadBuffer::~OutputReadBuffer()’:
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/OutputReadBuffer.cpp:17:3: warning: ‘throw’ will always call ‘terminate’ [-Wterminate]
17 | throw "Elements left in buffer!";
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/OutputReadBuffer.cpp:17:3: note: in C++11 destructors default to ‘noexcept’
In file included from /usr/include/c++/10/map:60,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/SequenceProvider.h:9,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/SequenceProvider.cpp:5:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, _SequenceProvider::RefIdx>; _KeyOfValue = std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, _SequenceProvider::RefIdx> >]’:
/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, _SequenceProvider::RefIdx>, std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >, std::less<int>, std::allocator<std::pair<const int, _SequenceProvider::RefIdx> > >::const_iterator’ changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 84%] Building CXX object src/CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/ScoreBuffer.cpp
In file included from /usr/include/c++/10/map:61,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/SequenceProvider.h:9,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/SequenceProvider.cpp:5:
/usr/include/c++/10/bits/stl_map.h: In member function ‘virtual void _SequenceProvider::Init(bool)’:
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, _SequenceProvider::RefIdx>, std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >, std::less<int>, std::allocator<std::pair<const int, _SequenceProvider::RefIdx> > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, _SequenceProvider::RefIdx>, std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >, std::less<int>, std::allocator<std::pair<const int, _SequenceProvider::RefIdx> > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, _SequenceProvider::RefIdx>, std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >, std::less<int>, std::allocator<std::pair<const int, _SequenceProvider::RefIdx> > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, _SequenceProvider::RefIdx>, std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >, std::less<int>, std::allocator<std::pair<const int, _SequenceProvider::RefIdx> > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, _SequenceProvider::RefIdx>, std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >, std::less<int>, std::allocator<std::pair<const int, _SequenceProvider::RefIdx> > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, _SequenceProvider::RefIdx>, std::_Select1st<std::pair<const int, _SequenceProvider::RefIdx> >, std::less<int>, std::allocator<std::pair<const int, _SequenceProvider::RefIdx> > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[ 88%] Building CXX object src/CMakeFiles/ngmlr.dir/StrippedSW.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/StrippedSW.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/StrippedSW.cpp
[ 92%] Building CXX object src/CMakeFiles/ngmlr.dir/unix.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/unix.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/unix.cpp
[ 96%] Building CXX object src/CMakeFiles/ngmlr.dir/unix_threads.cpp.o
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/usr/include/htslib -I/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/../lib -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ngmlr.dir/unix_threads.cpp.o -c /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/unix_threads.cpp
In file included from /usr/include/c++/10/map:60,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/unix.cpp:17:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, std::pair<const char*, long long unsigned int> >; _KeyOfValue = std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > >]’:
/usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/src/unix.cpp:17:
/usr/include/c++/10/bits/stl_map.h: In function ‘const int CreateMapping(const char*, const char*&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In function ‘uloc GetMapLength(int)’:
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In function ‘void Remap(int, const char*&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In function ‘void CloseMapping(int)’:
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, std::pair<const char*, long long unsigned int> >, std::_Select1st<std::pair<const int, std::pair<const char*, long long unsigned int> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<const char*, long long unsigned int> > > >::const_iterator’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[100%] Linking CXX executable ../../bin/ngmlr-0.2.7/ngmlr
cd /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngmlr.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/ngmlr-0.2.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ngmlr.dir/AlignmentMatrix.cpp.o CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o CMakeFiles/ngmlr.dir/ArgParser.cpp.o CMakeFiles/ngmlr.dir/CS.cpp.o CMakeFiles/ngmlr.dir/CSstatic.cpp.o CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o CMakeFiles/ngmlr.dir/LinearRegression.cpp.o CMakeFiles/ngmlr.dir/Logging.cpp.o CMakeFiles/ngmlr.dir/MappedRead.cpp.o CMakeFiles/ngmlr.dir/main.cpp.o CMakeFiles/ngmlr.dir/NGM.cpp.o CMakeFiles/ngmlr.dir/NGMTask.cpp.o CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o CMakeFiles/ngmlr.dir/PrefixTable.cpp.o CMakeFiles/ngmlr.dir/ReadProvider.cpp.o CMakeFiles/ngmlr.dir/SamParser.cpp.o CMakeFiles/ngmlr.dir/SAMWriter.cpp.o CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o CMakeFiles/ngmlr.dir/StrippedSW.cpp.o CMakeFiles/ngmlr.dir/unix.cpp.o CMakeFiles/ngmlr.dir/unix_threads.cpp.o -o ../../bin/ngmlr-0.2.7/ngmlr -lz -lpthread -lssw
make[3]: Leaving directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
[100%] Built target ngmlr
make[2]: Leaving directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
dh_auto_test -a -O--buildsystem=cmake
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dh_testroot -a -O--buildsystem=cmake
dh_prep -a -O--buildsystem=cmake
dh_auto_install -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<BUILDDIR>>/ngmlr-0.2.7\+dfsg/debian/ngmlr AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/ngmlr-0.2.7+dfsg -B/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
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Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<BUILDDIR>>/ngmlr-0.2.7+dfsg/debian/ngmlr/usr/bin/ngmlr
make[1]: Leaving directory '/<<BUILDDIR>>/ngmlr-0.2.7+dfsg/obj-arm-linux-gnueabihf'
dh_installdocs -a -O--buildsystem=cmake
dh_installchangelogs -a -O--buildsystem=cmake
dh_installexamples -a -O--buildsystem=cmake
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dpkg-shlibdeps: warning: debian/ngmlr/usr/bin/ngmlr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ngmlr/usr/bin/ngmlr was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
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dpkg-deb: building package 'ngmlr' in '../ngmlr_0.2.7+dfsg-4_armhf.deb'.
dpkg-deb: building package 'ngmlr-dbgsym' in '../ngmlr-dbgsym_0.2.7+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../ngmlr_0.2.7+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-12-14T08:40:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
ngmlr_0.2.7+dfsg-4_armhf.changes:
---------------------------------
Format: 1.8
Date: Sun, 06 Dec 2020 18:38:52 +0530
Source: ngmlr
Binary: ngmlr ngmlr-dbgsym
Architecture: armhf
Version: 0.2.7+dfsg-4
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
ngmlr - CoNvex Gap-cost alignMents for Long Reads
Changes:
ngmlr (0.2.7+dfsg-4) unstable; urgency=medium
.
* Update Build-Deps
* Attempt using simde to make portable across other arches
* Add simde flags
* Arch:any
* Fix va_list incompatibilities
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Files:
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a524a4f43a44d44f3a8a6446b99fa048 6022 science optional ngmlr_0.2.7+dfsg-4_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
ngmlr-dbgsym_0.2.7+dfsg-4_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 1238132 bytes: control archive=536 bytes.
373 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: ngmlr-dbgsym
Source: ngmlr
Version: 0.2.7+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1309
Depends: ngmlr (= 0.2.7+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for ngmlr
Build-Ids: ac6b06d6ae448dcb804e9281761f7e31dfc94aee
drwxr-xr-x root/root 0 2020-12-06 13:08 ./
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/lib/
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lrwxrwxrwx root/root 0 2020-12-06 13:08 ./usr/share/doc/ngmlr-dbgsym -> ngmlr
ngmlr_0.2.7+dfsg-4_armhf.deb
----------------------------
new Debian package, version 2.0.
size 649124 bytes: control archive=1652 bytes.
951 bytes, 18 lines control
2406 bytes, 30 lines md5sums
Package: ngmlr
Version: 0.2.7+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1069
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libssw0 (>= 1.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://github.com/philres/ngmlr
Description: CoNvex Gap-cost alignMents for Long Reads
Ngmlr is a long-read mapper designed to sensitively align PacBilo or
Oxford Nanopore to (large) reference genomes. It was designed to quickly
and correctly align the reads, including those spanning (complex)
structural variations. Ngmlr uses an SV aware k-mer search to find
approximate mapping locations for a read and then a banded Smith-
Waterman alignment algorithm to compute the final alignment. Ngmlr uses
a convex gap cost model that penalizes gap extensions for longer gaps
less than for shorter ones to compute precise alignments.
drwxr-xr-x root/root 0 2020-12-06 13:08 ./
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/bin/
-rwxr-xr-x root/root 357972 2020-12-06 13:08 ./usr/bin/ngmlr
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/share/
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/share/doc/ngmlr/
-rw-r--r-- root/root 3056 2018-06-25 08:11 ./usr/share/doc/ngmlr/README.md.gz
-rw-r--r-- root/root 278 2020-12-06 12:54 ./usr/share/doc/ngmlr/README.test
-rw-r--r-- root/root 434 2020-12-06 13:08 ./usr/share/doc/ngmlr/changelog.Debian.gz
-rw-r--r-- root/root 1554 2020-12-06 12:54 ./usr/share/doc/ngmlr/copyright
drwxr-xr-x root/root 0 2020-12-06 13:08 ./usr/share/doc/ngmlr/examples/
drwxr-xr-x root/root 0 2018-06-25 08:11 ./usr/share/doc/ngmlr/examples/data/
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-rw-r--r-- root/root 333 2018-06-25 08:11 ./usr/share/doc/ngmlr/examples/data/test_2/result.bed
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-rwxr-xr-x root/root 641 2018-06-25 08:11 ./usr/share/doc/ngmlr/examples/test_1.sh
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-rwxr-xr-x root/root 609 2018-06-25 08:11 ./usr/share/doc/ngmlr/examples/test_6.sh
-rwxr-xr-x root/root 198 2018-06-25 08:11 ./usr/share/doc/ngmlr/examples/test_travis.sh
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-rw-r--r-- root/root 1670 2020-12-06 13:08 ./usr/share/man/man1/ngmlr.1.gz
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 19072
Build-Time: 168
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 469
Job: ngmlr_0.2.7+dfsg-4
Machine Architecture: armhf
Package: ngmlr
Package-Time: 685
Source-Version: 0.2.7+dfsg-4
Space: 19072
Status: successful
Version: 0.2.7+dfsg-4
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Finished at 2020-12-14T08:40:23Z
Build needed 00:11:25, 19072k disc space