hhsuite →
3.3.0+ds-7 →
armhf → 2022-10-31 08:24:51
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| hhsuite 3.3.0+ds-7 (armhf) Mon, 31 Oct 2022 08:04:37 +0000 |
+==============================================================================+
Package: hhsuite
Version: 3.3.0+ds-7
Source Version: 3.3.0+ds-7
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-f977494a-4913-4921-9aa8-ba49cec6a361' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/hhsuite-QvGVAh/resolver-qEJnHF' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.6 MB in 15s (1850 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'hhsuite' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/hhsuite.git
Please use:
git clone https://salsa.debian.org/med-team/hhsuite.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4794 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main hhsuite 3.3.0+ds-7 (dsc) [2126 B]
Get:2 http://172.17.4.1/private bookworm-staging/main hhsuite 3.3.0+ds-7 (tar) [4775 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main hhsuite 3.3.0+ds-7 (diff) [16.6 kB]
Fetched 4794 kB in 1s (6997 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hhsuite-QvGVAh/hhsuite-3.3.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hhsuite-QvGVAh' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [394 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [478 B]
Fetched 1829 B in 0s (39.9 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap libperl5.34 perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file fontconfig-config fonts-dejavu-core gettext gettext-base
groff-base help2man hicolor-icon-theme imagemagick imagemagick-6-common
imagemagick-6.q16 intltool-debian libaom3 libarchive-zip-perl libarchive13
libbrotli1 libbsd0 libcurl4 libdav1d6 libde265-0 libdebhelper-perl
libdeflate0 libelf1 libexpat1 libfftw3-double3
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libheif1 libicu71 libjbig0 libjpeg62-turbo libjsoncpp25 liblcms2-2 liblerc4
liblocale-gettext-perl liblqr-1-0 libltdl7 libmagic-mgc libmagic1
libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmd0 libncurses6 libnghttp2-14
libopenjp2-7 libpipeline1 libpng16-16 libprocps8 libpsl5 librhash0 librtmp1
libsimde-dev libssh2-1 libsub-override-perl libtiff5 libtool libuchardet0
libuv1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx265-199
libxau6 libxcb1 libxdmcp6 libxext6 libxml2 m4 man-db po-debconf procps ucf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
cmake-format dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
imagemagick-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp
gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance
sane-utils texlive-base-bin transfig ufraw-batch xdg-utils lrzip
libfftw3-bin libfftw3-dev liblcms2-utils libmagickcore-6.q16-6-extra
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libmagickcore-6.q16-6-extra ghostscript netpbm
ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs gsfonts libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file fontconfig-config fonts-dejavu-core gettext gettext-base
groff-base help2man hicolor-icon-theme imagemagick imagemagick-6-common
imagemagick-6.q16 intltool-debian libaom3 libarchive-zip-perl libarchive13
libbrotli1 libbsd0 libcurl4 libdav1d6 libde265-0 libdebhelper-perl
libdeflate0 libelf1 libexpat1 libfftw3-double3
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libheif1 libicu71 libjbig0 libjpeg62-turbo libjsoncpp25 liblcms2-2 liblerc4
liblocale-gettext-perl liblqr-1-0 libltdl7 libmagic-mgc libmagic1
libmagickcore-6.q16-6 libmagickwand-6.q16-6 libmd0 libncurses6 libnghttp2-14
libopenjp2-7 libpipeline1 libpng16-16 libprocps8 libpsl5 librhash0 librtmp1
libsimde-dev libssh2-1 libsub-override-perl libtiff5 libtool libuchardet0
libuv1 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx265-199
libxau6 libxcb1 libxdmcp6 libxext6 libxml2 m4 man-db po-debconf procps
sbuild-build-depends-main-dummy ucf
0 upgraded, 90 newly installed, 0 to remove and 28 not upgraded.
Need to get 38.6 MB of archives.
After this operation, 157 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf liblocale-gettext-perl armhf 1.07-4+b3 [14.6 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.9-1 [83.3 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.38-2 [273 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libaom3 armhf 3.5.0-1 [1302 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libdav1d6 armhf 1.0.0-2+rpi1 [205 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libde265-0 armhf 1.0.8-1+rpi1+b1 [220 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libx265-199 armhf 3.5-2 [548 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libheif1 armhf 1.13.0-1 [169 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.13.1-1 [125 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.0-3 [1211 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.1 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.7-4 [399 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libopenjp2-7 armhf 2.5.0-1 [165 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-2 [133 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2 [237 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-4 [290 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libwebpdemux2 armhf 1.2.2-2 [97.1 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libwebpmux3 armhf 1.2.2-2 [105 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf imagemagick-6-common all 8:6.9.11.60+dfsg-1.3 [211 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libmagickcore-6.q16-6 armhf 8:6.9.11.60+dfsg-1.3+b4 [1607 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libmagickwand-6.q16-6 armhf 8:6.9.11.60+dfsg-1.3+b4 [385 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7.1 [41.9 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7.1 [457 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.0-1 [306 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.85.0-1 [325 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.2-1+rpi1 [125 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.14 [11.5 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.24.2-1 [2019 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.24.2-1 [3661 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf help2man armhf 1.49.2 [202 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.3+b4 [339 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf imagemagick armhf 8:6.9.11.60+dfsg-1.3+b4 [121 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libsimde-dev all 0.7.2-6 [259 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 16658 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-4+b3_armhf.deb ...
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Setting up libwebp7:armhf (1.2.2-2) ...
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Setting up libuchardet0:armhf (0.0.7-1) ...
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Setting up libssh2-1:armhf (1.10.0-3+b1) ...
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Setting up libtiff5:armhf (4.4.0-4) ...
Setting up libde265-0:armhf (1.0.8-1+rpi1+b1) ...
Setting up libwebpmux3:armhf (1.2.2-2) ...
Setting up libbsd0:armhf (0.11.7-1) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up liblocale-gettext-perl (1.07-4+b3) ...
Setting up libprocps8:armhf (2:3.3.17-7.1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
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Setting up fontconfig-config (2.13.1-4.5) ...
Setting up libwebpdemux2:armhf (1.2.2-2) ...
Setting up libheif1:armhf (1.13.0-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.2) ...
Setting up dh-autoreconf (20) ...
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14+20220924-2) ...
Setting up groff-base (1.22.4-8) ...
Setting up procps (2:3.3.17-7.1) ...
Setting up libcurl4:armhf (7.85.0-1) ...
Setting up libx11-6:armhf (2:1.8.1-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.11.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up cmake (3.24.2-1) ...
Setting up debhelper (13.10.1) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up libmagickcore-6.q16-6:armhf (8:6.9.11.60+dfsg-1.3+b4) ...
Setting up libmagickwand-6.q16-6:armhf (8:6.9.11.60+dfsg-1.3+b4) ...
Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.3+b4) ...
update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode
update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode
update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode
update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode
update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode
update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode
update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode
update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode
update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode
update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode
update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode
update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode
update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode
update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode
update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode
update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode
update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode
update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode
update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode
update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode
update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode
update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up imagemagick (8:6.9.11.60+dfsg-1.3+b4) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: hhsuite
Binary: hhsuite, hhsuite-data
Architecture: any all
Version: 3.3.0+ds-7
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lkajan@debian.org>, Andreas Tille <tille@debian.org>, Sascha Steinbiss <satta@debian.org>
Homepage: https://toolkit.tuebingen.mpg.de/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/hhsuite
Vcs-Git: https://salsa.debian.org/med-team/hhsuite.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man
Package-List:
hhsuite deb science optional arch=any
hhsuite-data deb science optional arch=all
Checksums-Sha1:
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8bcaea6473f306a2fd933a9a9913f59be81463d0 16620 hhsuite_3.3.0+ds-7.debian.tar.xz
Checksums-Sha256:
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72afa4e99e4dac312524f018329616f43a252e66f0e633446116e86f2020a037 16620 hhsuite_3.3.0+ds-7.debian.tar.xz
Files:
d01293f2b8337f9b914b30976c2a87e9 4775072 hhsuite_3.3.0+ds.orig.tar.xz
c1a253ee57acd5f059da2fd33ad6763d 16620 hhsuite_3.3.0+ds-7.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.pRkQIo8q/trustedkeys.kbx': General error
gpgv: Signature made Tue Oct 25 13:36:26 2022 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./hhsuite_3.3.0+ds-7.dsc
dpkg-source: info: extracting hhsuite in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking hhsuite_3.3.0+ds.orig.tar.xz
dpkg-source: info: unpacking hhsuite_3.3.0+ds-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying test_without_mpi
dpkg-source: info: applying perlscript_uselib
dpkg-source: info: applying perl_interpreter
dpkg-source: info: applying drop-fmemopen.h.patch
dpkg-source: info: applying python3
dpkg-source: info: applying ppc64el.patch
dpkg-source: info: applying exe_suffix
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=79d111ecf76d4d72929efb4c6c309344
JOURNAL_STREAM=8:26624
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-f977494a-4913-4921-9aa8-ba49cec6a361
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c153725
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package hhsuite
dpkg-buildpackage: info: source version 3.3.0+ds-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 build-* mybuild
find . -name "*.rej" -delete
find . -name "*~" -delete
dh_clean
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0
cd mybuild && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DNATIVE_ARCH=0 ..
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- 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
-- Compiler is GNU
-- Looking for fmemopen
-- Looking for fmemopen - found
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
-- xxd not found, using xxdi.pl instead
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /<<PKGBUILDDIR>>/mybuild
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --builddirectory mybuild
cd mybuild && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/mybuild --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/mybuild/CMakeFiles /<<PKGBUILDDIR>>/mybuild//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend
make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend
make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend
make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/data /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/data /<<PKGBUILDDIR>>/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
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make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build
make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build
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make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 1%] Generating ../generated/context_data.crf.h
cd /<<PKGBUILDDIR>>/data && mkdir -p /<<PKGBUILDDIR>>/mybuild/generated
[ 2%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o
[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex.c
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/hhviterbialgorithm.cpp
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/hhviterbialgorithm.cpp
cd /<<PKGBUILDDIR>>/data && /<<PKGBUILDDIR>>/cmake/xxdi.pl context_data.crf > /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h
/<<PKGBUILDDIR>>/lib/ffindex/src/ffindex.c: In function ‘ffindex_index_parse’:
/<<PKGBUILDDIR>>/lib/ffindex/src/ffindex.c:291:43: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
291 | fprintf(stderr, "Failed to allocate %ld bytes\n", nbytes);
| ~~^ ~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
[ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffutil.c
[ 6%] Linking C static library libffindex.a
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1
/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o
/usr/bin/ranlib libffindex.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 6%] Built target ffindex
[ 7%] Generating ../generated/context_data.lib.h
cd /<<PKGBUILDDIR>>/data && mkdir -p /<<PKGBUILDDIR>>/mybuild/generated
cd /<<PKGBUILDDIR>>/data && /<<PKGBUILDDIR>>/cmake/xxdi.pl context_data.lib > /<<PKGBUILDDIR>>/mybuild/generated/context_data.lib.h
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned char!' < /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h > /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h.tmp
cd /<<PKGBUILDDIR>>/data && mv -f /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h.tmp /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h
make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/hhviterbialgorithm.cpp
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned char!' < /<<PKGBUILDDIR>>/mybuild/generated/context_data.lib.h > /<<PKGBUILDDIR>>/mybuild/generated/context_data.lib.h.tmp
cd /<<PKGBUILDDIR>>/data && mv -f /<<PKGBUILDDIR>>/mybuild/generated/context_data.lib.h.tmp /<<PKGBUILDDIR>>/mybuild/generated/context_data.lib.h
[ 9%] Generating ../generated/cs219.lib.h
cd /<<PKGBUILDDIR>>/data && mkdir -p /<<PKGBUILDDIR>>/mybuild/generated
cd /<<PKGBUILDDIR>>/data && /<<PKGBUILDDIR>>/cmake/xxdi.pl cs219.lib > /<<PKGBUILDDIR>>/mybuild/generated/cs219.lib.h
cd /<<PKGBUILDDIR>>/data && /bin/sed 's!unsigned char!static const unsigned char!' < /<<PKGBUILDDIR>>/mybuild/generated/cs219.lib.h > /<<PKGBUILDDIR>>/mybuild/generated/cs219.lib.h.tmp
cd /<<PKGBUILDDIR>>/data && mv -f /<<PKGBUILDDIR>>/mybuild/generated/cs219.lib.h.tmp /<<PKGBUILDDIR>>/mybuild/generated/cs219.lib.h
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make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cs /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src/cs /<<PKGBUILDDIR>>/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color=
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[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /<<PKGBUILDDIR>>/src/cs/aa.cc
[ 11%] Linking CXX static library libhhviterbialgorithm_with_celloff.a
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a
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make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color=
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[ 11%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /<<PKGBUILDDIR>>/src/a3m_compress.cpp
[ 12%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a
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[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /<<PKGBUILDDIR>>/src/cs/as.cc
make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 14%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_apply_mpi.c
/<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_apply_mpi.c: In function ‘ffindex_apply_by_entry’:
/<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_apply_mpi.c:172:42: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
| ~~^ ~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
/<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_apply_mpi.c:172:47: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
| ~~^ ~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
/<<PKGBUILDDIR>>/src/a3m_compress.cpp: In function ‘std::string& rtrim(std::string&)’:
/<<PKGBUILDDIR>>/src/a3m_compress.cpp:504:43: warning: ‘std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]’ is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
504 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /<<PKGBUILDDIR>>/src/a3m_compress.h:11,
from /<<PKGBUILDDIR>>/src/a3m_compress.cpp:8:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
[ 15%] Linking C executable ffindex_apply
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 15%] Built target ffindex_apply
[ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /<<PKGBUILDDIR>>/src/cs/assert_helpers.cc
[ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /<<PKGBUILDDIR>>/src/cs/blosum_matrix.cc
[ 18%] Linking CXX static library libhhviterbialgorithm_and_ss.a
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_and_ss.a
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[ 18%] Built target hhviterbialgorithm_and_ss
[ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /<<PKGBUILDDIR>>/src/cs/getopt_pp.cc
make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake --color=
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[ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_reduce.c
[ 21%] Linking CXX static library libA3M_COMPRESS.a
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cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1
/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o
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[ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /<<PKGBUILDDIR>>/src/cs/log.cc
[ 23%] Linking C executable ffindex_reduce
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/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a
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[ 24%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /<<PKGBUILDDIR>>/src/cs/application.cc
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color=
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[ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_build.c
make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake --color=
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[ 26%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_from_fasta.c
[ 27%] Linking C executable ffindex_build
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/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a
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make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake --color=
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a
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[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_get.c
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color=
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[ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_modify.c
[ 31%] Linking C executable ffindex_get
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a
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make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color=
[ 32%] Linking C executable ffindex_modify
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1
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make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build
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/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a
[ 33%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_unpack.c
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make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color=
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[ 34%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_order.c
[ 35%] Linking C executable ffindex_unpack
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a
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make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake --color=
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[ 36%] Linking C executable ffindex_order
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1
[ 37%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /<<PKGBUILDDIR>>/lib/ffindex/src/ffindex_from_fasta_with_split.c
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a
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make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 38%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /<<PKGBUILDDIR>>/src/a3m_extract.cpp
[ 39%] Linking C executable ffindex_from_fasta_with_split
cd /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a
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[ 39%] Built target ffindex_from_fasta_with_split
make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake --color=
[ 40%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /<<PKGBUILDDIR>>/src/a3m_reduce.cpp
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[ 41%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /<<PKGBUILDDIR>>/src/a3m_database_reduce.cpp
[ 42%] Linking CXX static library libCS_OBJECTS.a
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/mybuild/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1
/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o
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make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake --color=
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make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 43%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /<<PKGBUILDDIR>>/src/a3m_database_extract.cpp
[ 44%] Linking CXX executable a3m_extract
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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[ 44%] Built target a3m_extract
make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake --color=
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make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 45%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /<<PKGBUILDDIR>>/src/a3m_database_filter.cpp
[ 46%] Linking CXX executable a3m_reduce
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
[ 47%] Linking CXX executable a3m_database_reduce
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 47%] Built target a3m_reduce
make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake --color=
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make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build
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[ 48%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 48%] Built target a3m_database_reduce
[ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /<<PKGBUILDDIR>>/src/hhdecl.cpp
[ 50%] Linking CXX executable a3m_database_extract
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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[ 50%] Built target a3m_database_extract
[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /<<PKGBUILDDIR>>/src/hhhit.cpp
[ 52%] Linking CXX executable a3m_database_filter
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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[ 52%] Built target a3m_database_filter
[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /<<PKGBUILDDIR>>/src/hhmatrices.cpp
[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /<<PKGBUILDDIR>>/src/hhsearch.cpp
[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /<<PKGBUILDDIR>>/src/hhalign.cpp
[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /<<PKGBUILDDIR>>/src/hhhitlist.cpp
[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /<<PKGBUILDDIR>>/src/hhposteriordecoder.cpp
[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /<<PKGBUILDDIR>>/src/hhutil.cpp
[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /<<PKGBUILDDIR>>/src/util.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/hhhit.h:14,
from /<<PKGBUILDDIR>>/src/hhhitlist.h:16,
from /<<PKGBUILDDIR>>/src/hhhitlist.cpp:9:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Hit>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]’,
inlined from ‘void HitList::PrintMatrices(HMM*, std::stringstream&, bool, size_t, const float (*)[20])’ at /<<PKGBUILDDIR>>/src/hhhitlist.cpp:591:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /<<PKGBUILDDIR>>/src/hhalignment.cpp
[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/hhforwardalgorithm.cpp
[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /<<PKGBUILDDIR>>/src/hhhmm.cpp
[ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /<<PKGBUILDDIR>>/src/hhposteriordecoderrunner.cpp
[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/hhviterbialgorithm.cpp
/<<PKGBUILDDIR>>/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’:
/<<PKGBUILDDIR>>/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=]
1797 | sprintf(details, "The alingment %s does not contain any sequences.",
| ^~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<PKGBUILDDIR>>/src/hhalignment.h:6,
from /<<PKGBUILDDIR>>/src/hhalignment.cpp:8:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’ at /<<PKGBUILDDIR>>/src/hhalignment.cpp:1797:14:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /<<PKGBUILDDIR>>/src/hhfullalignment.cpp
[ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /<<PKGBUILDDIR>>/src/hhhmmsimd.cpp
[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /<<PKGBUILDDIR>>/src/hhposteriormatrix.cpp
[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /<<PKGBUILDDIR>>/src/hhviterbi.cpp
[ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /<<PKGBUILDDIR>>/src/hhbacktracemac.cpp
[ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/hhmacalgorithm.cpp
[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /<<PKGBUILDDIR>>/src/hhprefilter.cpp
[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /<<PKGBUILDDIR>>/src/hhviterbimatrix.cpp
[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /<<PKGBUILDDIR>>/src/hhbackwardalgorithm.cpp
[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/ffindexdatabase.cpp
[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/hhdatabase.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from /<<PKGBUILDDIR>>/lib/simd/simd.h:9,
from /<<PKGBUILDDIR>>/src/util.h:23,
from /<<PKGBUILDDIR>>/src/hhhmm.h:8,
from /<<PKGBUILDDIR>>/src/hhprefilter.h:17,
from /<<PKGBUILDDIR>>/src/hhprefilter.cpp:8:
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Distance = int; _Tp = pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /<<PKGBUILDDIR>>/src/hhhalfalignment.cpp
[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /<<PKGBUILDDIR>>/src/hhviterbirunner.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/hhprefilter.h:11:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<double, int> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘_ZN9Prefilter12prefilter_dbEP3HMMP4HashI3HitEiiiiiddiiiPA20_KfRSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaISH_EESK_._omp_fn.1’ at /<<PKGBUILDDIR>>/src/hhprefilter.cpp:531:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’:
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1625 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /<<PKGBUILDDIR>>/src/hhfunc.cpp
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = comparePair]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘void Prefilter::prefilter_db(HMM*, Hash<Hit>*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&, std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&)’ at /<<PKGBUILDDIR>>/src/hhprefilter.cpp:536:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = comparePair]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘void Prefilter::prefilter_db(HMM*, Hash<Hit>*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&, std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&)’ at /<<PKGBUILDDIR>>/src/hhprefilter.cpp:536:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<PKGBUILDDIR>>/src/util.h:20,
from /<<PKGBUILDDIR>>/src/hhhmm.h:8,
from /<<PKGBUILDDIR>>/src/hhhmmsimd.h:5,
from /<<PKGBUILDDIR>>/src/hhviterbirunner.h:4,
from /<<PKGBUILDDIR>>/src/hhviterbirunner.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Hit>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]’,
inlined from ‘void ViterbiConsumerThread::align(int, int, float, char)’ at /<<PKGBUILDDIR>>/src/hhviterbirunner.cpp:67:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]’,
inlined from ‘void ViterbiRunner::merge_thread_results(std::vector<Hit>&, std::vector<HHEntry*>&, std::map<std::__cxx11::basic_string<char>, std::vector<Viterbi::BacktraceResult> >&, std::vector<ViterbiConsumerThread*>&, int, float)’ at /<<PKGBUILDDIR>>/src/hhviterbirunner.cpp:259:31,
inlined from ‘std::vector<Hit> ViterbiRunner::alignment(Parameters&, HMMSimd*, std::vector<HHEntry*>, float, float*, const float (*)[20], const float (*)[20], const float (*)[20], int, const float (*)[4][11], const float (*)[11][4][11], const float (*)[11][8])’ at /<<PKGBUILDDIR>>/src/hhviterbirunner.cpp:173:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]’,
inlined from ‘void ViterbiRunner::merge_thread_results(std::vector<Hit>&, std::vector<HHEntry*>&, std::map<std::__cxx11::basic_string<char>, std::vector<Viterbi::BacktraceResult> >&, std::vector<ViterbiConsumerThread*>&, int, float)’ at /<<PKGBUILDDIR>>/src/hhviterbirunner.cpp:259:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 79%] Linking CXX static library libHH_OBJECTS.a
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1
/usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o
/usr/bin/ranlib libHH_OBJECTS.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 79%] Built target HH_OBJECTS
make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend
make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend
make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend
make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhmake.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhfilter.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build
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make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build
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make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 81%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o
[ 81%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c /<<PKGBUILDDIR>>/src/hhfilter.cpp
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake.dir/hhmake.cpp.o -MF CMakeFiles/hhmake.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake.dir/hhmake.cpp.o -c /<<PKGBUILDDIR>>/src/hhmake.cpp
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cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits_app.cpp
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits.dir/hhblits_app.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits_app.cpp
[ 84%] Linking CXX executable hhsearch
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
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[ 86%] Building CXX object src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign.dir/hhblits_app.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits_app.cpp
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cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhconsensus.dir/DependInfo.cmake --color=
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[ 87%] Building CXX object src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -c /<<PKGBUILDDIR>>/src/hhconsensus.cpp
[ 88%] Linking CXX executable hhfilter
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
[ 89%] Linking CXX executable hhmake
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 89%] Built target hhfilter
make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake --color=
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make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build
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[ 90%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c /<<PKGBUILDDIR>>/src/cs/cstranslate_app.cc
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[ 90%] Built target hhmake
make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake --color=
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make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 91%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits_omp.cpp
[ 92%] Linking CXX executable hhalign
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 92%] Built target hhalign
make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhsearch_omp.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 93%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits_omp.cpp
[ 94%] Linking CXX executable hhconsensus
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
/<<PKGBUILDDIR>>/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<PKGBUILDDIR>>/src/hhblits.h:11,
from /<<PKGBUILDDIR>>/src/hhsearch.h:34,
from /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:8:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘void OutputFFIndex::close()’ at /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:26:17,
inlined from ‘int main(int, const char**)’ at /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:167:33:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 94%] Built target hhconsensus
make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 95%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits_omp.cpp
[ 96%] Linking CXX executable hhblits_omp
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 96%] Built target hhblits_omp
make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
cd /<<PKGBUILDDIR>>/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/src /<<PKGBUILDDIR>>/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 97%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<PKGBUILDDIR>>/mybuild/generated -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/lib/ffindex/src -I/<<PKGBUILDDIR>>/lib/simde -I/<<PKGBUILDDIR>>/lib/simd -I/<<PKGBUILDDIR>>/mybuild/src -I/<<PKGBUILDDIR>>/src/cs -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /<<PKGBUILDDIR>>/src/hhblits_ca3m.cpp
/<<PKGBUILDDIR>>/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<PKGBUILDDIR>>/src/hhblits.h:11,
from /<<PKGBUILDDIR>>/src/hhsearch.h:34,
from /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:8:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘void OutputFFIndex::close()’ at /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:26:17,
inlined from ‘int main(int, const char**)’ at /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:167:33:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 98%] Linking CXX executable hhsearch_omp
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 98%] Built target hhsearch_omp
/<<PKGBUILDDIR>>/src/hhblits_omp.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/src/hhblits_omp.cpp:26:51: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<PKGBUILDDIR>>/src/hhblits.h:11,
from /<<PKGBUILDDIR>>/src/hhsearch.h:34,
from /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:8:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘void OutputFFIndex::close()’ at /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:26:17,
inlined from ‘int main(int, const char**)’ at /<<PKGBUILDDIR>>/src/hhblits_omp.cpp:167:33:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 99%] Linking CXX executable hhalign_omp
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
/<<PKGBUILDDIR>>/src/hhblits_ca3m.cpp: In function ‘int main(int, const char**)’:
/<<PKGBUILDDIR>>/src/hhblits_ca3m.cpp:24:49: warning: ‘.ffindex’ directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<PKGBUILDDIR>>/src/hhblits.h:11,
from /<<PKGBUILDDIR>>/src/hhblits_ca3m.cpp:8:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘void OutputFFIndex::close()’ at /<<PKGBUILDDIR>>/src/hhblits_ca3m.cpp:24:15,
inlined from ‘int main(int, const char**)’ at /<<PKGBUILDDIR>>/src/hhblits_ca3m.cpp:358:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:54:35: note: ‘__builtin___snprintf_chk’ output between 9 and 4104 bytes into a destination of size 4096
54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
55 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 99%] Built target hhalign_omp
[100%] Linking CXX executable hhblits_ca3m
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[100%] Built target hhblits_ca3m
[100%] Linking CXX executable cstranslate
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[100%] Built target cstranslate
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/mybuild/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd /<<PKGBUILDDIR>>/data && PATH=$PATH:/<<PKGBUILDDIR>>/mybuild/src:/<<PKGBUILDDIR>>/mybuild/lib/ffindex/src ./test.sh
- 08:21:07.055 INFO: query.a3m is in A2M, A3M or FASTA format
- 08:21:08.743 INFO: Alternative alignment: 0
- 08:21:08.919 INFO: 1 alignments done
- 08:21:09.039 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 49 out of 118
Neff 4.29223
Searched_HMMs 1
Date Mon Oct 31 08:21:09 2022
Command hhalign -i query.a3m -o result.hhr -t query.a3m
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431)
query.a3m 0 32127 1571 0
query.a3m 0 32666 13 0
query.a3m 0 32666 446 0
Reading context library for pseudocounts from internal ...
Reading abstract state alphabet from internal ...
Processing entry: query.a3m
Adding cs-pseudocounts (admix=0.30) ...
- 08:21:14.485 INFO: Searching 1 column state sequences.
- 08:21:14.822 INFO: query.a3m is in A2M, A3M or FASTA format
- 08:21:14.911 INFO: Iteration 1
- 08:21:16.050 INFO: Prefiltering database
- 08:21:17.262 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 08:21:17.277 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 08:21:17.278 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 08:21:17.278 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 08:21:17.638 INFO: Alternative alignment: 0
- 08:21:17.808 INFO: 1 alignments done
- 08:21:17.808 INFO: Alternative alignment: 1
- 08:21:17.977 INFO: 1 alignments done
- 08:21:17.977 INFO: Alternative alignment: 2
- 08:21:17.977 INFO: Alternative alignment: 3
- 08:21:19.408 INFO: Premerge done
- 08:21:19.408 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 08:21:19.604 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 59 out of 118
Neff 4.27431
Searched_HMMs 1
Date Mon Oct 31 08:21:19 2022
Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431)
2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431)
- 08:21:19.700 INFO: Searching 1 column state sequences.
- 08:21:19.001 INFO: Thread 0 query.a3m
- 08:21:20.093 INFO: query.a3m is in A2M, A3M or FASTA format
- 08:21:20.184 INFO: Iteration 1
- 08:21:22.175 INFO: Prefiltering database
- 08:21:24.156 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 08:21:24.169 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 08:21:24.169 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 08:21:24.170 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 08:21:24.349 INFO: Alternative alignment: 0
- 08:21:24.518 INFO: 1 alignments done
- 08:21:24.518 INFO: Alternative alignment: 1
- 08:21:24.686 INFO: 1 alignments done
- 08:21:24.686 INFO: Alternative alignment: 2
- 08:21:24.686 INFO: Alternative alignment: 3
- 08:21:26.850 INFO: Premerge done
- 08:21:26.851 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 08:21:26.989 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
- 08:21:27.501 INFO: query.a3m is in A2M, A3M or FASTA format
- 08:21:27.590 INFO: Searching 1 database HHMs without prefiltering
- 08:21:27.590 INFO: Iteration 1
- 08:21:28.932 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 08:21:29.292 INFO: Alternative alignment: 0
- 08:21:29.461 INFO: 1 alignments done
- 08:21:29.461 INFO: Alternative alignment: 1
- 08:21:29.629 INFO: 1 alignments done
- 08:21:29.630 INFO: Alternative alignment: 2
- 08:21:29.630 INFO: Alternative alignment: 3
- 08:21:31.261 INFO: Premerge done
- 08:21:31.262 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 08:21:31.455 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3
Match_columns 431
No_of_seqs 49 out of 118
Neff 4.29223
Searched_HMMs 1
Date Mon Oct 31 08:21:31 2022
Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431)
2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431)
- 08:21:31.817 INFO: Thread 0 query.a3m
- 08:21:31.923 INFO: query.a3m is in A2M, A3M or FASTA format
- 08:21:32.021 INFO: Searching 1 database HHMs without prefiltering
- 08:21:32.021 INFO: Iteration 1
- 08:21:34.047 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 08:21:34.228 INFO: Alternative alignment: 0
- 08:21:34.397 INFO: 1 alignments done
- 08:21:34.398 INFO: Alternative alignment: 1
- 08:21:34.565 INFO: 1 alignments done
- 08:21:34.565 INFO: Alternative alignment: 2
- 08:21:34.566 INFO: Alternative alignment: 3
- 08:21:36.757 INFO: Premerge done
- 08:21:36.757 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 08:21:36.898 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/hhsuite/usr/libexec/hhsuite/bin
dh_auto_install --builddirectory mybuild
cd mybuild && make -j4 install DESTDIR=/<<BUILDDIR>>/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/mybuild --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_reduce
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_apply
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_build
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_from_fasta
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_get
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_modify
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_unpack
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_order
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/ffindex_from_fasta_with_split
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/context_data.crf
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/context_data.lib
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/cs219.lib
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete.phr
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete.pin
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/data/do_not_delete.psq
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhblits
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhfilter
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhsearch
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhalign
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhconsensus
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_extract
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_reduce
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_database_reduce
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_database_extract
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/a3m_database_filter
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/cstranslate
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhblits_omp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhsearch_omp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhalign_omp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/hhblits_ca3m
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/a3m.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/addss.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/Align.pm
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/check_a3m.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/cif2fasta.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/create_profile_from_hhm.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/create_profile_from_hmmer.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/ffindex.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/get_a3m_size.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hh_reader.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hhmakemodel.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hhmakemodel.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/HHPaths.pm
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/hhsuitedb.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/mergeali.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/multithread.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/pdb2fasta.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/pdbfilter.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/pdbfilter.py
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/reformat.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/renumberpdb.pl
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/scripts/splitfasta.pl
make[2]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
for prog in hhalign hhalign_omp hhblits hhblits_omp hhblits_ca3m hhconsensus hhfilter hhmake hhsearch hhsearch_omp a3m_extract a3m_reduce a3m_database_reduce a3m_database_extract a3m_database_filter ; do dh_install -phhsuite usr/bin/${prog} usr/bin/ ; done
dh_install -phhsuite usr/bin/cstranslate* usr/libexec/hhsuite/bin
dh_install -phhsuite usr/bin/ffindex_* usr/bin/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhblits_omp" 'debian/tmp/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1'
export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.3.0+ds -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1'
dh_installman --arch
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhfilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhconsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhmake contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_ca3m contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_omp 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/hhsuite/usr/bin/hhfilter debian/hhsuite/usr/bin/hhsearch debian/hhsuite/usr/bin/hhconsensus debian/hhsuite/usr/bin/a3m_database_filter debian/hhsuite/usr/bin/ffindex_from_fasta_with_split debian/hhsuite/usr/bin/a3m_extract debian/hhsuite/usr/bin/ffindex_unpack debian/hhsuite/usr/bin/ffindex_modify debian/hhsuite/usr/bin/hhmake debian/hhsuite/usr/bin/hhsearch_omp debian/hhsuite/usr/bin/ffindex_reduce debian/hhsuite/usr/bin/ffindex_get debian/hhsuite/usr/bin/a3m_database_extract debian/hhsuite/usr/bin/a3m_database_reduce debian/hhsuite/usr/bin/ffindex_from_fasta debian/hhsuite/usr/bin/hhblits debian/hhsuite/usr/bin/hhalign_omp debian/hhsuite/usr/bin/a3m_reduce debian/hhsuite/usr/bin/hhblits_ca3m debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate debian/hhsuite/usr/bin/ffindex_apply debian/hhsuite/usr/bin/ffindex_order debian/hhsuite/usr/bin/hhalign debian/hhsuite/usr/bin/ffindex_build debian/hhsuite/usr/bin/hhblits_omp were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-6), "
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-7_armhf.deb'.
dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-7_armhf.deb'.
dpkg-genbuildinfo --build=any -O../hhsuite_3.3.0+ds-7_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../hhsuite_3.3.0+ds-7_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-10-31T08:24:36Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
hhsuite_3.3.0+ds-7_armhf.changes:
---------------------------------
Format: 1.8
Date: Tue, 25 Oct 2022 15:17:24 +0200
Source: hhsuite
Binary: hhsuite hhsuite-dbgsym
Architecture: armhf
Version: 3.3.0+ds-7
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
Changes:
hhsuite (3.3.0+ds-7) unstable; urgency=medium
.
* Fix watchfile.
* Bump Standards-Version.
* Update date in d/copyright.
Checksums-Sha1:
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7e1dc35867c12f38f787a30dc20862cdd64bb36e 7010 hhsuite_3.3.0+ds-7_armhf.buildinfo
34d308d4ee7b86632bbf9c326ad8b4246b6a71ff 10232780 hhsuite_3.3.0+ds-7_armhf.deb
Checksums-Sha256:
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a9a13e6e5c49c86642e220cc43cd467737c872e6e7669190201acc7ebf012ee4 7010 hhsuite_3.3.0+ds-7_armhf.buildinfo
9dee09c42948c23c3af3e30d915534b2e86ee004effe805cc4034b9ecd63ec68 10232780 hhsuite_3.3.0+ds-7_armhf.deb
Files:
db10a3005ae006b4f786824e9b4229ba 17673200 debug optional hhsuite-dbgsym_3.3.0+ds-7_armhf.deb
d945afd41fdaf5231b16db7310408690 7010 science optional hhsuite_3.3.0+ds-7_armhf.buildinfo
0caeac9f0b8ff2c01f8e2b44276c2a7e 10232780 science optional hhsuite_3.3.0+ds-7_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: hhsuite
Binary: hhsuite hhsuite-dbgsym
Architecture: armhf
Version: 3.3.0+ds-7
Checksums-Md5:
db10a3005ae006b4f786824e9b4229ba 17673200 hhsuite-dbgsym_3.3.0+ds-7_armhf.deb
0caeac9f0b8ff2c01f8e2b44276c2a7e 10232780 hhsuite_3.3.0+ds-7_armhf.deb
Checksums-Sha1:
725240084ac0bbcb36dcca10db13ac3b873f9d96 17673200 hhsuite-dbgsym_3.3.0+ds-7_armhf.deb
34d308d4ee7b86632bbf9c326ad8b4246b6a71ff 10232780 hhsuite_3.3.0+ds-7_armhf.deb
Checksums-Sha256:
58a8af5576f0255b8e29f997c52b22706c235601a96a0b1aed6b5151bc974ba7 17673200 hhsuite-dbgsym_3.3.0+ds-7_armhf.deb
9dee09c42948c23c3af3e30d915534b2e86ee004effe805cc4034b9ecd63ec68 10232780 hhsuite_3.3.0+ds-7_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 31 Oct 2022 08:24:33 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-9),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2~rc2-2),
binutils (= 2.39-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.39-6+rpi1),
binutils-common (= 2.39-6+rpi1),
bsdextrautils (= 2.38.1-1.1),
bsdutils (= 1:2.38.1-1.1),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
cmake (= 3.24.2-1),
cmake-data (= 3.24.2-1),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-3+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.79),
debhelper (= 13.10.1),
debianutils (= 5.7-0.3),
dh-autoreconf (= 20),
dh-elpa-helper (= 2.0.14),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.8-1),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.14+20220924-2),
emacsen-common (= 3.0.4),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
fontconfig-config (= 2.13.1-4.5),
fonts-dejavu-core (= 2.37-2),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-3+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-3+rpi1),
gcc-12-base (= 12.2.0-3+rpi1),
gettext (= 0.21-9),
gettext-base (= 0.21-9),
grep (= 3.7-1),
groff-base (= 1.22.4-8),
gzip (= 1.12-1),
help2man (= 1.49.2),
hicolor-icon-theme (= 0.17-2),
hostname (= 3.23),
imagemagick (= 8:6.9.11.60+dfsg-1.3+b4),
imagemagick-6-common (= 8:6.9.11.60+dfsg-1.3),
imagemagick-6.q16 (= 8:6.9.11.60+dfsg-1.3+b4),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-1),
libaom3 (= 3.5.0-1),
libarchive-zip-perl (= 1.68-1),
libarchive13 (= 3.6.0-1),
libasan8 (= 12.2.0-3+rpi1),
libatomic1 (= 12.2.0-3+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbinutils (= 2.39-6+rpi1),
libblkid1 (= 2.38.1-1.1),
libbrotli1 (= 1.0.9-2+b2),
libbsd0 (= 0.11.7-1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.35-2+rpi1),
libc-dev-bin (= 2.35-2+rpi1),
libc6 (= 2.35-2+rpi1),
libc6-dev (= 2.35-2+rpi1),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 12.2.0-3+rpi1),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.28-2),
libcrypt1 (= 1:4.4.28-2),
libctf-nobfd0 (= 2.39-6+rpi1),
libctf0 (= 2.39-6+rpi1),
libcurl4 (= 7.85.0-1),
libdav1d6 (= 1.0.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libde265-0 (= 1.0.8-1+rpi1+b1),
libdebconfclient0 (= 0.264),
libdebhelper-perl (= 13.10.1),
libdeflate0 (= 1.14-1),
libdpkg-perl (= 1.21.9+rpi1),
libelf1 (= 0.187-2+rpi2),
libexpat1 (= 2.4.9-1),
libffi8 (= 3.4.2-4),
libfftw3-double3 (= 3.3.8-2),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libfontconfig1 (= 2.13.1-4.5),
libfreetype6 (= 2.12.1+dfsg-3),
libgcc-12-dev (= 12.2.0-3+rpi1),
libgcc-s1 (= 12.2.0-3+rpi1),
libgcrypt20 (= 1.10.1-2+b2),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libglib2.0-0 (= 2.74.0-3),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgnutls30 (= 3.7.8-2),
libgomp1 (= 12.2.0-3+rpi1),
libgpg-error0 (= 1.45-2),
libgssapi-krb5-2 (= 1.20-1),
libheif1 (= 1.13.0-1),
libhogweed6 (= 3.8.1-2),
libicu71 (= 71.1-3),
libidn2-0 (= 2.3.3-1),
libisl23 (= 0.25-1),
libjbig0 (= 2.1-3.1+b2),
libjpeg62-turbo (= 1:2.1.2-1),
libjsoncpp25 (= 1.9.5-4),
libk5crypto3 (= 1.20-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20-1),
libkrb5support0 (= 1.20-1),
liblcms2-2 (= 2.13.1-1),
libldap-2.5-0 (= 2.5.13+dfsg-2+rpi1),
liblerc4 (= 4.0.0+ds-2),
liblocale-gettext-perl (= 1.07-4+b3),
liblqr-1-0 (= 0.4.2-2.1),
libltdl7 (= 2.4.7-4),
liblz4-1 (= 1.9.4-1+rpi1),
liblzma5 (= 5.2.5-2.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmagickcore-6.q16-6 (= 8:6.9.11.60+dfsg-1.3+b4),
libmagickwand-6.q16-6 (= 8:6.9.11.60+dfsg-1.3+b4),
libmd0 (= 1.0.4-2),
libmount1 (= 2.38.1-1.1),
libmpc3 (= 1.2.1-2),
libmpfr6 (= 4.1.0-3),
libncurses6 (= 6.3+20220423-2),
libncursesw6 (= 6.3+20220423-2),
libnettle8 (= 3.8.1-2),
libnghttp2-14 (= 1.50.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libopenjp2-7 (= 2.5.0-1),
libp11-kit0 (= 0.24.1-1),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpcre2-8-0 (= 10.40-1+b2),
libpcre3 (= 2:8.39-14),
libperl5.36 (= 5.36.0-4),
libpipeline1 (= 1.5.6-3),
libpng16-16 (= 1.6.38-2),
libprocps8 (= 2:3.3.17-7.1),
libpsl5 (= 0.21.0-1.2),
librhash0 (= 1.4.3-3),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg-8),
libsasl2-modules-db (= 2.1.28+dfsg-8),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsimde-dev (= 0.7.2-6),
libsmartcols1 (= 2.38.1-1.1),
libssh2-1 (= 1.10.0-3+b1),
libssl3 (= 3.0.5-4),
libstdc++-12-dev (= 12.2.0-3+rpi1),
libstdc++6 (= 12.2.0-3+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 251.5-1+rpi1),
libtasn1-6 (= 4.19.0-2),
libtiff5 (= 4.4.0-4),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-4),
libubsan1 (= 12.2.0-3+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 251.5-1+rpi1),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-1.1),
libuv1 (= 1.44.2-1+rpi1),
libwebp7 (= 1.2.2-2),
libwebpdemux2 (= 1.2.2-2),
libwebpmux3 (= 1.2.2-2),
libx11-6 (= 2:1.8.1-2),
libx11-data (= 2:1.8.1-2),
libx265-199 (= 3.5-2),
libxau6 (= 1:1.0.9-1),
libxcb1 (= 1.15-1),
libxdmcp6 (= 1:1.1.2-3),
libxext6 (= 2:1.3.4-1),
libxml2 (= 2.9.14+dfsg-1),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 5.19.6-1+rpi1),
login (= 1:4.12.3+dfsg1-1),
m4 (= 1.4.19-1),
make (= 4.3-4.1),
man-db (= 2.11.0-1),
mawk (= 1.3.4.20200120-3.1),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
patch (= 2.7.6-7),
perl (= 5.36.0-4),
perl-base (= 5.36.0-4),
perl-modules-5.36 (= 5.36.0-4),
po-debconf (= 1.0.21+nmu1),
procps (= 2:3.3.17-7.1),
rpcsvc-proto (= 1.4.2-4),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sgml-base (= 1.31),
sysvinit-utils (= 3.05-6),
tar (= 1.34+dfsg-1),
ucf (= 3.0043),
util-linux (= 2.38.1-1.1),
util-linux-extra (= 2.38.1-1.1),
xz-utils (= 5.2.5-2.1),
zlib1g (= 1:1.2.11.dfsg-4.1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1666703844"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
hhsuite-dbgsym_3.3.0+ds-7_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 17673200 bytes: control archive=1744 bytes.
1362 bytes, 12 lines control
2737 bytes, 26 lines md5sums
Package: hhsuite-dbgsym
Source: hhsuite
Version: 3.3.0+ds-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18288
Depends: hhsuite (= 3.3.0+ds-7)
Section: debug
Priority: optional
Description: debug symbols for hhsuite
Build-Ids: 2016d7b6c2363de6b5bf2548765559ea4568f468 203ad348de17d9bdd9376894362eadb415902555 344a483f1338865c682bbb5871dcdc6bfde1ad1a 3abdcaab5b4dbc006c8931c7ae3d38c8c5185c43 4906f654f2d712963e7596a69faa9d746e605e8f 6201dfc52f36d6ad1772c7f5802ed8ef6e1fa2f7 6c412e40b6cb05983321cc50e5f19656e523aa24 72ac8e1fbb968e07cd0aa62543d21b1a9603d83d 8ef79275f1b8fc3f8b71239720265ff0ba2f77f4 8f3bbca1e90e23cc95db8f64b96bb5344635964e 9e586e2ea1092290c3d48beac7cb0c09af46eefd a65589ce3baf71db5a46c659e73bc00d84bc223c a9d3e66ee6bc3eea4da812ef5085c7f1d049a7fe ada4898dc75fd22cea56027610d5478de888f04d b2f068bf8e6fcabf546265278dd19dae61213f22 b83f0a59694bd933e2d0fdef59fe0ff3e629d3d0 c0573b0a5e0eb03bed93ca65f1ebbfdf8cf6fd67 cdac944d56f47c5f6384ed6d64bbab2918cfcd22 d5a9082026a9146b420c0554e763b32925b46be9 d7396bac4ea239e05ca5cc319703055d76585ea3 da1e9a19eeeee183907a85ed111d9f67e12040ae db79456bab92dfc36d749a9f8952446237e15495 de6e456c3aae7f2a4c50e590dc54d38a16496e9c f47b79684ee848ae6ff73f6022cd178efe172d4d fc3482cdb78519abce91d6aba6f7886a47e974fa
drwxr-xr-x root/root 0 2022-10-25 13:17 ./
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/debug/.build-id/20/
-rw-r--r-- root/root 24504 2022-10-25 13:17 ./usr/lib/debug/.build-id/20/16d7b6c2363de6b5bf2548765559ea4568f468.debug
-rw-r--r-- root/root 23028 2022-10-25 13:17 ./usr/lib/debug/.build-id/20/3ad348de17d9bdd9376894362eadb415902555.debug
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/debug/.build-id/34/
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lrwxrwxrwx root/root 0 2022-10-25 13:17 ./usr/share/doc/hhsuite-dbgsym -> hhsuite
hhsuite_3.3.0+ds-7_armhf.deb
----------------------------
new Debian package, version 2.0.
size 10232780 bytes: control archive=2824 bytes.
1471 bytes, 29 lines control
4311 bytes, 65 lines md5sums
Package: hhsuite
Version: 3.3.0+ds-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 77469
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 11), perl:any, hhsuite-data (= 3.3.0+ds-7), python3
Conflicts: ffindex
Built-Using: simde (= 0.7.2-6)
Section: science
Priority: optional
Homepage: https://toolkit.tuebingen.mpg.de/
Description: sensitive protein sequence searching based on HMM-HMM alignment
HH-suite is an open-source software package for sensitive protein sequence
searching based on the pairwise alignment of hidden Markov models (HMMs).
.
This package contains HHsearch and HHblits among other programs and utilities.
.
HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM
and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
proteins. HHsearch is often used for protein structure prediction to detect
homologous templates and to build highly accurate query-template pairwise
alignments for homology modeling.
.
HHblits can build high-quality MSAs starting from single sequences or from
MSAs. It transforms these into a query HMM and, using an iterative search
strategy, adds significantly similar sequences from the previous search to
the updated query HMM for the next search iteration. Compared to PSI-BLAST,
HHblits is faster, up to twice as sensitive and produces more accurate
alignments.
drwxr-xr-x root/root 0 2022-10-25 13:17 ./
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/bin/
-rwxr-xr-x root/root 67220 2022-10-25 13:17 ./usr/bin/a3m_database_extract
-rwxr-xr-x root/root 67220 2022-10-25 13:17 ./usr/bin/a3m_database_filter
-rwxr-xr-x root/root 67220 2022-10-25 13:17 ./usr/bin/a3m_database_reduce
-rwxr-xr-x root/root 67220 2022-10-25 13:17 ./usr/bin/a3m_extract
-rwxr-xr-x root/root 67220 2022-10-25 13:17 ./usr/bin/a3m_reduce
-rwxr-xr-x root/root 67248 2022-10-25 13:17 ./usr/bin/ffindex_apply
-rwxr-xr-x root/root 67280 2022-10-25 13:17 ./usr/bin/ffindex_build
-rwxr-xr-x root/root 67216 2022-10-25 13:17 ./usr/bin/ffindex_from_fasta
-rwxr-xr-x root/root 67168 2022-10-25 13:17 ./usr/bin/ffindex_from_fasta_with_split
-rwxr-xr-x root/root 67200 2022-10-25 13:17 ./usr/bin/ffindex_get
-rwxr-xr-x root/root 67248 2022-10-25 13:17 ./usr/bin/ffindex_modify
-rwxr-xr-x root/root 67168 2022-10-25 13:17 ./usr/bin/ffindex_order
-rwxr-xr-x root/root 67168 2022-10-25 13:17 ./usr/bin/ffindex_reduce
-rwxr-xr-x root/root 67168 2022-10-25 13:17 ./usr/bin/ffindex_unpack
-rwxr-xr-x root/root 7997088 2022-10-25 13:17 ./usr/bin/hhalign
-rwxr-xr-x root/root 7997088 2022-10-25 13:17 ./usr/bin/hhalign_omp
-rwxr-xr-x root/root 7997088 2022-10-25 13:17 ./usr/bin/hhblits
-rwxr-xr-x root/root 7997088 2022-10-25 13:17 ./usr/bin/hhblits_ca3m
-rwxr-xr-x root/root 7997088 2022-10-25 13:17 ./usr/bin/hhblits_omp
-rwxr-xr-x root/root 7538332 2022-10-25 13:17 ./usr/bin/hhconsensus
-rwxr-xr-x root/root 329368 2022-10-25 13:17 ./usr/bin/hhfilter
-rwxr-xr-x root/root 7538332 2022-10-25 13:17 ./usr/bin/hhmake
-rwxr-xr-x root/root 7997088 2022-10-25 13:17 ./usr/bin/hhsearch
-rwxr-xr-x root/root 7997088 2022-10-25 13:17 ./usr/bin/hhsearch_omp
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/
lrwxrwxrwx root/root 0 2022-10-25 13:17 ./usr/lib/hh -> hhsuite
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/hhsuite/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/lib/hhsuite/data/
-rw-r--r-- root/root 1986 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete
-rw-r--r-- root/root 135 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete.phr
-rw-r--r-- root/root 112 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete.pin
-rw-r--r-- root/root 433 2020-08-16 23:16 ./usr/lib/hhsuite/data/do_not_delete.psq
lrwxrwxrwx root/root 0 2022-10-25 13:17 ./usr/lib/hhsuite/scripts -> ../../share/hhsuite/scripts
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/libexec/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/libexec/hhsuite/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/libexec/hhsuite/bin/
-rwxr-xr-x root/root 6227624 2022-10-25 13:17 ./usr/libexec/hhsuite/bin/cstranslate
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/doc/hhsuite/
-rw-r--r-- root/root 1986 2020-08-16 23:16 ./usr/share/doc/hhsuite/README.md.gz
-rw-r--r-- root/root 1727 2022-10-25 13:17 ./usr/share/doc/hhsuite/changelog.Debian.gz
-rw-r--r-- root/root 20399 2022-10-25 13:17 ./usr/share/doc/hhsuite/copyright
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/doc/hhsuite/examples/
-rw-r--r-- root/root 32126 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.a3m
-rw-r--r-- root/root 57578 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.hhm
-rw-r--r-- root/root 181765 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.hhr
-rw-r--r-- root/root 506 2020-08-16 23:16 ./usr/share/doc/hhsuite/examples/query.seq
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/hhsuite/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/hhsuite/scripts/
-rw-r--r-- root/root 24577 2020-08-16 23:16 ./usr/share/hhsuite/scripts/Align.pm
-rw-r--r-- root/root 4710 2020-08-16 23:16 ./usr/share/hhsuite/scripts/HHPaths.pm
-rwxr-xr-x root/root 8021 2022-10-25 13:17 ./usr/share/hhsuite/scripts/a3m.py
-rwxr-xr-x root/root 31681 2022-10-25 13:17 ./usr/share/hhsuite/scripts/addss.pl
-rwxr-xr-x root/root 438 2022-10-25 13:17 ./usr/share/hhsuite/scripts/check_a3m.py
-rwxr-xr-x root/root 28735 2022-10-25 13:17 ./usr/share/hhsuite/scripts/cif2fasta.py
-rwxr-xr-x root/root 4654 2022-10-25 13:17 ./usr/share/hhsuite/scripts/create_profile_from_hhm.pl
-rwxr-xr-x root/root 6815 2022-10-25 13:17 ./usr/share/hhsuite/scripts/create_profile_from_hmmer.pl
-rwxr-xr-x root/root 2081 2022-10-25 13:17 ./usr/share/hhsuite/scripts/ffindex.py
-rwxr-xr-x root/root 446 2022-10-25 13:17 ./usr/share/hhsuite/scripts/get_a3m_size.py
-rwxr-xr-x root/root 7179 2022-10-25 13:17 ./usr/share/hhsuite/scripts/hh_reader.py
-rwxr-xr-x root/root 48079 2022-10-25 13:17 ./usr/share/hhsuite/scripts/hhmakemodel.pl
-rwxr-xr-x root/root 87343 2022-10-25 13:17 ./usr/share/hhsuite/scripts/hhmakemodel.py
-rwxr-xr-x root/root 16961 2022-10-25 13:17 ./usr/share/hhsuite/scripts/hhsuitedb.py
-rwxr-xr-x root/root 20214 2020-08-16 23:16 ./usr/share/hhsuite/scripts/mergeali.pl
-rwxr-xr-x root/root 5717 2022-10-25 13:17 ./usr/share/hhsuite/scripts/multithread.pl
-rwxr-xr-x root/root 40490 2022-10-25 13:17 ./usr/share/hhsuite/scripts/pdb2fasta.pl
-rwxr-xr-x root/root 13183 2022-10-25 13:17 ./usr/share/hhsuite/scripts/pdbfilter.pl
-rwxr-xr-x root/root 8648 2022-10-25 13:17 ./usr/share/hhsuite/scripts/pdbfilter.py
-rwxr-xr-x root/root 28328 2020-08-16 23:16 ./usr/share/hhsuite/scripts/reformat.pl
-rwxr-xr-x root/root 14019 2022-10-25 13:17 ./usr/share/hhsuite/scripts/renumberpdb.pl
-rwxr-xr-x root/root 3651 2022-10-25 13:17 ./usr/share/hhsuite/scripts/splitfasta.pl
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/man/
drwxr-xr-x root/root 0 2022-10-25 13:17 ./usr/share/man/man1/
-rw-r--r-- root/root 3091 2022-10-25 13:17 ./usr/share/man/man1/hhalign.1.gz
-rw-r--r-- root/root 4142 2022-10-25 13:17 ./usr/share/man/man1/hhblits.1.gz
-rw-r--r-- root/root 4152 2022-10-25 13:17 ./usr/share/man/man1/hhblits_omp.1.gz
-rw-r--r-- root/root 1029 2022-10-25 13:17 ./usr/share/man/man1/hhconsensus.1.gz
-rw-r--r-- root/root 1022 2022-10-25 13:17 ./usr/share/man/man1/hhfilter.1.gz
-rw-r--r-- root/root 1656 2022-10-25 13:17 ./usr/share/man/man1/hhmake.1.gz
-rw-r--r-- root/root 3359 2022-10-25 13:17 ./usr/share/man/man1/hhsearch.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 576592
Build-Time: 570
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 577
Job: hhsuite_3.3.0+ds-7
Machine Architecture: armhf
Package: hhsuite
Package-Time: 1199
Source-Version: 3.3.0+ds-7
Space: 576592
Status: successful
Version: 3.3.0+ds-7
--------------------------------------------------------------------------------
Finished at 2022-10-31T08:24:36Z
Build needed 00:19:59, 576592k disk space