hhsuite →
3.3.0+ds-8+b1 →
armhf → 2024-02-07 23:18:47
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| hhsuite 3.3.0+ds-8+b1 (armhf) Wed, 07 Feb 2024 23:14:37 +0000 |
+==============================================================================+
Package: hhsuite
Version: 3.3.0+ds-8+b1
Source Version: 3.3.0+ds-8
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-8596bb47-0176-49b0-acaa-bebb245b4063' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/hhsuite-kx4eG0/resolver-MOTpbx' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
Fetched 29.5 MB in 5s (5541 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-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 trixie-staging/main hhsuite 3.3.0+ds-8 (dsc) [2271 B]
Get:2 http://172.17.4.1/private trixie-staging/main hhsuite 3.3.0+ds-8 (tar) [4775 kB]
Get:3 http://172.17.4.1/private trixie-staging/main hhsuite 3.3.0+ds-8 (diff) [16.9 kB]
Fetched 4794 kB in 1s (7666 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hhsuite-kx4eG0/hhsuite-3.3.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hhsuite-kx4eG0' 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 [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [661 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [693 B]
Fetched 1963 B in 0s (0 B/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 additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config
fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base help2man
hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16
intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbsd0 libcurl4
libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libelf1 libexpat1
libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1
libfreetype6 libglib2.0-0 libheif-plugin-dav1d libheif-plugin-libde265
libheif1 libicu72 libjbig0 libjpeg62-turbo libjsoncpp25 liblcms2-2 liblerc4
liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-7
libmagickwand-6.q16-7 libnghttp2-14 libopenjp2-7 libpipeline1 libpng16-16
libproc2-0 libpsl5 libraw23 librhash0 librtmp1 libsharpyuv0 libsimde-dev
libssh2-1 libsub-override-perl libtiff6 libtool libuchardet0 libuv1 libwebp7
libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
libxext6 libxml2 m4 man-db po-debconf procps sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff imagemagick-6-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 libraw-bin
xdg-utils lrzip libfftw3-bin libfftw3-dev low-memory-monitor
libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc
libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e
libheif-plugin-svtenc liblcms2-utils libmagickcore-6.q16-7-extra libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libmagickcore-6.q16-7-extra ghostscript netpbm
ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libheif-plugin-aomenc libheif-plugin-x265 fonts-urw-base35
publicsuffix libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config
fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base help2man
hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16
intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbsd0 libcurl4
libdav1d7 libde265-0 libdebhelper-perl libdeflate0 libelf1 libexpat1
libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1
libfreetype6 libglib2.0-0 libheif-plugin-dav1d libheif-plugin-libde265
libheif1 libicu72 libjbig0 libjpeg62-turbo libjsoncpp25 liblcms2-2 liblerc4
liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-7
libmagickwand-6.q16-7 libnghttp2-14 libopenjp2-7 libpipeline1 libpng16-16
libproc2-0 libpsl5 libraw23 librhash0 librtmp1 libsharpyuv0 libsimde-dev
libssh2-1 libsub-override-perl libtiff6 libtool libuchardet0 libuv1 libwebp7
libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6
libxext6 libxml2 m4 man-db po-debconf procps sbuild-build-depends-main-dummy
sensible-utils
0 upgraded, 88 newly installed, 0 to remove and 15 not upgraded.
Need to get 42.0 MB of archives.
After this operation, 155 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-3 [259 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [366 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.14.2-6 [316 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.14.2-6 [367 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libsharpyuv0 armhf 1.3.2-0.3 [106 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libdav1d7 armhf 1.3.0-2+rpi1 [214 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-dav1d armhf 1.17.6-1 [9300 B]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libde265-0 armhf 1.0.15-1+rpi1 [140 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-libde265 armhf 1.17.6-1 [12.2 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libheif1 armhf 1.17.6-1 [237 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf liblcms2-2 armhf 2.14-2 [124 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0 armhf 2.78.3-2 [1257 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.1 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libltdl7 armhf 2.4.7-7 [390 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libopenjp2-7 armhf 2.5.0-2+b2 [165 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libraw23 armhf 0.21.1-7+rpi1 [363 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.19-1 [39.0 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf liblerc4 armhf 4.0.0+ds-4 [132 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libwebp7 armhf 1.3.2-0.3 [261 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libtiff6 armhf 4.5.1+git230720-4 [299 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libwebpdemux2 armhf 1.3.2-0.3 [106 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libwebpmux3 armhf 1.3.2-0.3 [116 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.8-1 [120 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.7-1 [328 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.7-1 [729 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf imagemagick-6-common all 8:6.9.12.98+dfsg1-5 [66.9 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libmagickcore-6.q16-7 armhf 8:6.9.12.98+dfsg1-5+b1 [1516 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libmagickwand-6.q16-7 armhf 8:6.9.12.98+dfsg1-5+b1 [291 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libproc2-0 armhf 2:4.0.4-4 [54.8 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf procps armhf 2:4.0.4-4 [848 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libarchive13 armhf 3.7.2-1 [294 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.59.0-1 [61.9 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-4 [195 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 8.5.0-2+rpi1 [377 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libjsoncpp25 armhf 1.9.5-6 [64.7 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libuv1 armhf 1.46.0-3+rpi1 [129 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf cmake-data all 3.28.1-1 [2127 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf cmake armhf 3.28.1-1 [7787 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.13 [85.0 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.13 [889 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf help2man armhf 1.49.3 [198 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf imagemagick-6.q16 armhf 8:6.9.12.98+dfsg1-5+b1 [290 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf imagemagick armhf 8:6.9.12.98+dfsg1-5+b1 [19.5 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libsimde-dev all 0.7.6-1 [384 kB]
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Setting up autopoint (0.21-14) ...
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Setting up fonts-dejavu-core (2.37-8) ...
Setting up libltdl7:armhf (2.4.7-7) ...
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Setting up autoconf (2.71-3) ...
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Setting up libdav1d7:armhf (1.3.0-2+rpi1) ...
Setting up liblqr-1-0:armhf (0.4.2-2.1) ...
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Setting up libtiff6:armhf (4.5.1+git230720-4) ...
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Setting up procps (2:4.0.4-4) ...
Setting up libopenjp2-7:armhf (2.5.0-2+b2) ...
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Setting up libssh2-1:armhf (1.11.0-4) ...
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Setting up libraw23:armhf (0.21.1-7+rpi1) ...
Setting up libde265-0:armhf (1.0.15-1+rpi1) ...
Setting up libwebpmux3:armhf (1.3.2-0.3) ...
Setting up libbsd0:armhf (0.11.8-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
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 (1.13.1-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-14) ...
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Setting up fontconfig-config (2.14.2-6) ...
Setting up libwebpdemux2:armhf (1.3.2-0.3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libfreetype6:armhf (2.13.2+dfsg-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libcurl4:armhf (8.5.0-2+rpi1) ...
Setting up libx11-6:armhf (2:1.8.7-1) ...
Setting up libfontconfig1:armhf (2.14.2-6) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up cmake (3.28.1-1) ...
Setting up debhelper (13.13) ...
Setting up libheif-plugin-dav1d:armhf (1.17.6-1) ...
Setting up libheif-plugin-libde265:armhf (1.17.6-1) ...
Setting up libheif1:armhf (1.17.6-1) ...
Setting up libmagickcore-6.q16-7:armhf (8:6.9.12.98+dfsg1-5+b1) ...
Setting up libmagickwand-6.q16-7:armhf (8:6.9.12.98+dfsg1-5+b1) ...
Setting up imagemagick-6.q16 (8:6.9.12.98+dfsg1-5+b1) ...
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 (8:6.9.12.98+dfsg1-5+b1) ...
Processing triggers for libc-bin (2.37-13+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.2+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-13+rpi1 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 apt_2.7.9 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 cmake_3.28.1-1 cmake-data_3.28.1-1 coreutils_9.4-3 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.83 debhelper_13.13 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.2+rpi1 dpkg-dev_1.22.2+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 fontconfig-config_2.14.2-6 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: hhsuite
Binary: hhsuite, hhsuite-data
Architecture: any all
Version: 3.3.0+ds-8
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: 4.6.2
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:
d90462ba593366296d8916e184b42325caa4201b 4775072 hhsuite_3.3.0+ds.orig.tar.xz
0c6aa80d717ee79df31a05f33d2f461b1b6f0c88 16868 hhsuite_3.3.0+ds-8.debian.tar.xz
Checksums-Sha256:
a81037f2e2a4801f1a42f5aa5939334fe038053d05ceabdc0899fefb8cc00a44 4775072 hhsuite_3.3.0+ds.orig.tar.xz
d408a3d42581737068f06b96cd922c462f672beeb4faf94f41ac37340170b3cb 16868 hhsuite_3.3.0+ds-8.debian.tar.xz
Files:
d01293f2b8337f9b914b30976c2a87e9 4775072 hhsuite_3.3.0+ds.orig.tar.xz
81b05abfd099550bfb153063e218961e 16868 hhsuite_3.3.0+ds-8.debian.tar.xz
Dgit: 140af672217dfdd27cb9e04f647e16721cab7092 debian archive/debian/3.3.0+ds-8 https://git.dgit.debian.org/hhsuite
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gpgv: Signature made Sun Aug 13 09:54:49 2023 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-8.dsc: no acceptable signature found
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-8.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
dpkg-source: info: applying gcc-13.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 3.3.0+ds-8+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-8596bb47-0176-49b0-acaa-bebb245b4063
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package hhsuite
dpkg-buildpackage: info: source version 3.3.0+ds-8+b1
dpkg-buildpackage: info: source distribution trixie-staging
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 && DEB_PYTHON_INSTALL_LAYOUT=deb 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 ..
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- 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
CMake Deprecation Warning at lib/ffindex/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- 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 (2.3s)
-- Generating done (0.1s)
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>>/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src /<<PKGBUILDDIR>>/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color="
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="
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_with_celloff.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/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
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 -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
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'
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 4%] 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%] Generating ../generated/context_data.crf.h
[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
cd /<<PKGBUILDDIR>>/data && mkdir -p /<<PKGBUILDDIR>>/mybuild/generated
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 -fstack-clash-protection -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 -fstack-clash-protection -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>>/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 -fstack-clash-protection -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>>/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 -fstack-clash-protection -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
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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'
[ 7%] 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 -fstack-clash-protection -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
[ 8%] 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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[ 9%] Built target hhviterbialgorithm_with_celloff
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake
[ 10%] Generating ../generated/context_data.lib.h
cd /<<PKGBUILDDIR>>/data && mkdir -p /<<PKGBUILDDIR>>/mybuild/generated
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1
cd /<<PKGBUILDDIR>>/data && /<<PKGBUILDDIR>>/cmake/xxdi.pl context_data.lib > /<<PKGBUILDDIR>>/mybuild/generated/context_data.lib.h
/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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[ 11%] 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 && /usr/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
make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend
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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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[ 12%] 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 -fstack-clash-protection -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
[ 13%] 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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make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.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_COMPRESS.dir/DependInfo.cmake "--color="
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[ 13%] 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 -fstack-clash-protection -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
cd /<<PKGBUILDDIR>>/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h > /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h.tmp
[ 14%] 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 -fstack-clash-protection -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
/<<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++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from /<<PKGBUILDDIR>>/src/a3m_compress.h:11,
from /<<PKGBUILDDIR>>/src/a3m_compress.cpp:8:
/usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
cd /<<PKGBUILDDIR>>/data && mv -f /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h.tmp /<<PKGBUILDDIR>>/mybuild/generated/context_data.crf.h
[ 15%] 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 -fstack-clash-protection -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
[ 16%] 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 -fstack-clash-protection -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
[ 17%] 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 -fstack-clash-protection -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
[ 18%] Linking CXX static library libA3M_COMPRESS.a
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake
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
/usr/bin/ranlib libA3M_COMPRESS.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 18%] Built target A3M_COMPRESS
[ 19%] 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 -fstack-clash-protection -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
cd /<<PKGBUILDDIR>>/data && /usr/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
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[ 19%] Built target generated
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="
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make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 20%] 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 -fstack-clash-protection -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
make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.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_reduce.dir/DependInfo.cmake "--color="
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[ 21%] 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 -fstack-clash-protection -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
/<<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
make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend
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[ 22%] 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 -fstack-clash-protection -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
[ 23%] Linking C executable ffindex_reduce
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/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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%] 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
[ 24%] Built target ffindex_reduce
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
[ 25%] 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 -fstack-clash-protection -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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make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.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.dir/DependInfo.cmake "--color="
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[ 26%] Linking C executable ffindex_build
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[ 27%] 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 -fstack-clash-protection -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
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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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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="
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[ 28%] 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 -fstack-clash-protection -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
[ 29%] Linking C executable ffindex_from_fasta
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/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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%] Built target ffindex_from_fasta
make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.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_modify.dir/DependInfo.cmake "--color="
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[ 31%] 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 -fstack-clash-protection -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
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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="
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[ 32%] 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 -fstack-clash-protection -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
[ 33%] 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
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
[ 34%] 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
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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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[ 35%] 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 -fstack-clash-protection -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
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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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make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 36%] 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 -fstack-clash-protection -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
make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend
[ 37%] 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
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_extract.dir/DependInfo.cmake "--color="
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build
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 -fstack-clash-protection -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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 38%] Built target ffindex_order
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'
[ 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
[ 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 -fstack-clash-protection -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
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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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[ 40%] Built target ffindex_from_fasta_with_split
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="
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make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 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 -fstack-clash-protection -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
/usr/bin/ranlib libCS_OBJECTS.a
[ 43%] Linking CXX executable a3m_extract
cd /<<PKGBUILDDIR>>/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
[ 43%] Built target CS_OBJECTS
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="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 44%] 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 -fstack-clash-protection -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
[ 45%] 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 -fstack-clash-protection -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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 45%] 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="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 46%] 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 -fstack-clash-protection -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
[ 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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
[ 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
make[4]: Entering directory '/<<PKGBUILDDIR>>/mybuild'
[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/mybuild'
[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from /<<PKGBUILDDIR>>/src/hhhit.h:14,
from /<<PKGBUILDDIR>>/src/hhhitlist.h:16,
from /<<PKGBUILDDIR>>/src/hhhitlist.cpp:9:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<Hit>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1289 | _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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 ‘void Alignment::Read(FILE*, char*, char, int, int, char*)’:
/<<PKGBUILDDIR>>/src/hhalignment.cpp:251:38: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
251 | sprintf(cur_name, "no_name_%i", k);
| ^
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/13/cstdio:42,
from /usr/include/c++/13/ext/string_conversions.h:45,
from /usr/include/c++/13/bits/basic_string.h:4109,
from /usr/include/c++/13/string:54,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
from /<<PKGBUILDDIR>>/src/hhalignment.h:6,
from /<<PKGBUILDDIR>>/src/hhalignment.cpp:8:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void Alignment::Read(FILE*, char*, char, int, int, char*)’ at /<<PKGBUILDDIR>>/src/hhalignment.cpp:251:16:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 10 and 20 bytes into a destination of size 19
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 -fstack-clash-protection -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 -fstack-clash-protection -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
/<<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 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 ());
| ~~~~~~~~~~~~~~~~~
[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/bits/stl_algo.h:61,
from /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_algo.h:1812:5: 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
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: 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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/vector:72,
from /<<PKGBUILDDIR>>/src/hhprefilter.h:11:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<std::pair<double, int> >::iterator’ changed in GCC 7.1
445 | 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++/13/bits/stl_vector.h:1296:21,
inlined from ‘_ZN9Prefilter12prefilter_dbEP3HMMP4HashI3HitEiiiiiddiiiPA20_KfRSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaISH_EESK_._omp_fn.1’ at /<<PKGBUILDDIR>>/src/hhprefilter.cpp:531:21:
/usr/include/c++/13/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++/13/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++/13/bits/stl_algo.h:1631:5: 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
1631 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1631:5: 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++/13/bits/stl_algo.h:1631:5: 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++/13/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++/13/bits/stl_algo.h:1918:5: 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
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: 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
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++/13/bits/stl_algo.h:1926:27:
/usr/include/c++/13/bits/stl_algo.h:1910:25: 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
1910 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/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++/13/bits/stl_algo.h:1932:32: 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
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __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 -fstack-clash-protection -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++/13/bits/stl_algo.h:4894:18,
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++/13/bits/stl_algo.h:1947:32: 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
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __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++/13/bits/stl_algo.h:1950:31,
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++/13/bits/stl_algo.h:4894:18,
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++/13/bits/stl_algo.h:1859:32: 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
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: 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
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
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++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<Hit>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1289 | _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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1289 | _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++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >’ changed in GCC 7.1
1289 | _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/hhblits.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/hhfilter.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/hhmake.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/hhsearch.dir/DependInfo.cmake "--color="
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make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build
make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build
make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build
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[ 83%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o
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[ 83%] Building CXX object src/CMakeFiles/hhsearch.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 -fstack-clash-protection -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 -fstack-clash-protection -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
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 -fstack-clash-protection -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 -fstack-clash-protection -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
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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 -fstack-clash-protection -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 -fstack-clash-protection -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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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 -fstack-clash-protection -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
[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
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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 -fstack-clash-protection -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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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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[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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
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make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.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/hhsearch_omp.dir/DependInfo.cmake "--color="
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[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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
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[ 94%] Built target hhconsensus
make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.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/hhalign_omp.dir/DependInfo.cmake "--color="
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[ 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 -fstack-clash-protection -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
/<<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++/13/cstdio:42,
from /usr/include/c++/13/ext/string_conversions.h:45,
from /usr/include/c++/13/bits/basic_string.h:4109,
from /usr/include/c++/13/string:54,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
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 ());
| ~~~~~~~~~~~~~~~~~
[ 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 -fstack-clash-protection -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 -fstack-clash-protection -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++/13/cstdio:42,
from /usr/include/c++/13/ext/string_conversions.h:45,
from /usr/include/c++/13/bits/basic_string.h:4109,
from /usr/include/c++/13/string:54,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
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 -fstack-clash-protection -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++/13/cstdio:42,
from /usr/include/c++/13/ext/string_conversions.h:45,
from /usr/include/c++/13/bits/basic_string.h:4109,
from /usr/include/c++/13/string:54,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
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 -fstack-clash-protection -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++/13/cstdio:42,
from /usr/include/c++/13/ext/string_conversions.h:45,
from /usr/include/c++/13/bits/basic_string.h:4109,
from /usr/include/c++/13/string:54,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/istream:40,
from /usr/include/c++/13/fstream:40,
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 -fstack-clash-protection -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 -fstack-clash-protection -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
- 23:17:23.553 INFO: query.a3m is in A2M, A3M or FASTA format
- 23:17:24.076 INFO: Alternative alignment: 0
- 23:17:24.137 INFO: 1 alignments done
- 23:17:24.190 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 Wed Feb 7 23:17:24 2024
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 347 0
query.a3m 0 32666 5 0
query.a3m 0 32666 132 0
Reading context library for pseudocounts from internal ...
Reading abstract state alphabet from internal ...
Processing entry: query.a3m
Adding cs-pseudocounts (admix=0.30) ...
- 23:17:25.745 INFO: Searching 1 column state sequences.
- 23:17:25.842 INFO: query.a3m is in A2M, A3M or FASTA format
- 23:17:25.866 INFO: Iteration 1
- 23:17:26.190 INFO: Prefiltering database
- 23:17:26.507 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 23:17:26.514 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 23:17:26.514 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 23:17:26.514 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 23:17:26.633 INFO: Alternative alignment: 0
- 23:17:26.692 INFO: 1 alignments done
- 23:17:26.692 INFO: Alternative alignment: 1
- 23:17:26.745 INFO: 1 alignments done
- 23:17:26.745 INFO: Alternative alignment: 2
- 23:17:26.745 INFO: Alternative alignment: 3
- 23:17:27.185 INFO: Premerge done
- 23:17:27.185 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 23:17:27.255 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 Wed Feb 7 23:17:27 2024
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)
- 23:17:27.294 INFO: Searching 1 column state sequences.
- 23:17:27.374 INFO: Thread 0 query.a3m
- 23:17:27.406 INFO: query.a3m is in A2M, A3M or FASTA format
- 23:17:27.430 INFO: Iteration 1
- 23:17:28.076 INFO: Prefiltering database
- 23:17:28.713 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 23:17:28.718 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 23:17:28.719 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 23:17:28.719 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 23:17:28.776 INFO: Alternative alignment: 0
- 23:17:28.834 INFO: 1 alignments done
- 23:17:28.834 INFO: Alternative alignment: 1
- 23:17:28.887 INFO: 1 alignments done
- 23:17:28.887 INFO: Alternative alignment: 2
- 23:17:28.887 INFO: Alternative alignment: 3
- 23:17:29.590 INFO: Premerge done
- 23:17:29.590 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 23:17:29.634 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
- 23:17:29.776 INFO: query.a3m is in A2M, A3M or FASTA format
- 23:17:29.799 INFO: Searching 1 database HHMs without prefiltering
- 23:17:29.799 INFO: Iteration 1
- 23:17:30.143 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 23:17:30.259 INFO: Alternative alignment: 0
- 23:17:30.318 INFO: 1 alignments done
- 23:17:30.318 INFO: Alternative alignment: 1
- 23:17:30.372 INFO: 1 alignments done
- 23:17:30.372 INFO: Alternative alignment: 2
- 23:17:30.372 INFO: Alternative alignment: 3
- 23:17:30.854 INFO: Premerge done
- 23:17:30.855 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 23:17:30.935 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 Wed Feb 7 23:17:30 2024
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)
- 23:17:31.048 INFO: Thread 0 query.a3m
- 23:17:31.080 INFO: query.a3m is in A2M, A3M or FASTA format
- 23:17:31.104 INFO: Searching 1 database HHMs without prefiltering
- 23:17:31.104 INFO: Iteration 1
- 23:17:31.710 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 23:17:31.767 INFO: Alternative alignment: 0
- 23:17:31.826 INFO: 1 alignments done
- 23:17:31.826 INFO: Alternative alignment: 1
- 23:17:31.879 INFO: 1 alignments done
- 23:17:31.879 INFO: Alternative alignment: 2
- 23:17:31.879 INFO: Alternative alignment: 3
- 23:17:32.552 INFO: Premerge done
- 23:17:32.553 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 23:17:32.596 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/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/hhalign 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/a3m_database_filter debian/hhsuite/usr/bin/ffindex_get debian/hhsuite/usr/bin/hhmake debian/hhsuite/usr/bin/ffindex_unpack debian/hhsuite/usr/bin/ffindex_from_fasta debian/hhsuite/usr/bin/hhsearch_omp debian/hhsuite/usr/bin/hhalign_omp debian/hhsuite/usr/bin/ffindex_from_fasta_with_split debian/hhsuite/usr/bin/hhblits_omp debian/hhsuite/usr/bin/ffindex_order debian/hhsuite/usr/bin/hhalign debian/hhsuite/usr/bin/ffindex_build debian/hhsuite/usr/bin/a3m_extract debian/hhsuite/usr/bin/ffindex_modify debian/hhsuite/usr/bin/hhfilter debian/hhsuite/usr/bin/hhsearch debian/hhsuite/usr/bin/hhconsensus debian/hhsuite/usr/bin/a3m_database_extract debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate debian/hhsuite/usr/bin/a3m_database_reduce debian/hhsuite/usr/bin/a3m_reduce debian/hhsuite/usr/bin/ffindex_reduce debian/hhsuite/usr/bin/ffindex_apply debian/hhsuite/usr/bin/hhblits_ca3m debian/hhsuite/usr/bin/hhblits 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 (= 0.7.6-1), "
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8+b1_armhf.deb'.
dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8+b1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../hhsuite_3.3.0+ds-8+b1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../hhsuite_3.3.0+ds-8+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-02-07T23:18:40Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
hhsuite_3.3.0+ds-8+b1_armhf.changes:
------------------------------------
Format: 1.8
Date: Wed, 07 Feb 2024 23:15:51 +0000
Source: hhsuite (3.3.0+ds-8)
Binary: hhsuite hhsuite-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 3.3.0+ds-8+b1
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Raspbian pi5 test autobuilder <root@raspbian.org>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
Changes:
hhsuite (3.3.0+ds-8+b1) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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770dc7269323bc681dbb42710ecdf3684485f84b 7615 hhsuite_3.3.0+ds-8+b1_armhf.buildinfo
92b562848c3445c614d00e425496e7a8a422f43d 10241928 hhsuite_3.3.0+ds-8+b1_armhf.deb
Checksums-Sha256:
03c6d82ba7d3156df7853997eed082861b4d286b05b4f54cd5a763809dc1d61a 16990212 hhsuite-dbgsym_3.3.0+ds-8+b1_armhf.deb
6b7a580cc618a4327cc7fefee010a9c48c8bf2a5b39c6a496985c60e1f73470f 7615 hhsuite_3.3.0+ds-8+b1_armhf.buildinfo
bd2719292d85bfb484e14d9f7e6de84af0322aa80ffa16b37d36c0a51127faeb 10241928 hhsuite_3.3.0+ds-8+b1_armhf.deb
Files:
ff780750888b138f7078333d68569c4e 16990212 debug optional hhsuite-dbgsym_3.3.0+ds-8+b1_armhf.deb
5f976dcde634697de348cd0b90e4e240 7615 science optional hhsuite_3.3.0+ds-8+b1_armhf.buildinfo
4d96e94956a9807a098bbe35a0cb5537 10241928 science optional hhsuite_3.3.0+ds-8+b1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: hhsuite (3.3.0+ds-8)
Binary: hhsuite hhsuite-dbgsym
Architecture: armhf
Version: 3.3.0+ds-8+b1
Binary-Only-Changes:
hhsuite (3.3.0+ds-8+b1) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi5 test autobuilder <root@raspbian.org> Wed, 07 Feb 2024 23:15:51 +0000
Checksums-Md5:
ff780750888b138f7078333d68569c4e 16990212 hhsuite-dbgsym_3.3.0+ds-8+b1_armhf.deb
4d96e94956a9807a098bbe35a0cb5537 10241928 hhsuite_3.3.0+ds-8+b1_armhf.deb
Checksums-Sha1:
7b94233c2b18510ae4a8e83d97cd95db2e6cf370 16990212 hhsuite-dbgsym_3.3.0+ds-8+b1_armhf.deb
92b562848c3445c614d00e425496e7a8a422f43d 10241928 hhsuite_3.3.0+ds-8+b1_armhf.deb
Checksums-Sha256:
03c6d82ba7d3156df7853997eed082861b4d286b05b4f54cd5a763809dc1d61a 16990212 hhsuite-dbgsym_3.3.0+ds-8+b1_armhf.deb
bd2719292d85bfb484e14d9f7e6de84af0322aa80ffa16b37d36c0a51127faeb 10241928 hhsuite_3.3.0+ds-8+b1_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Wed, 07 Feb 2024 23:18:40 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.3),
bash (= 5.2.21-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-6),
bsdutils (= 1:2.39.3-6),
build-essential (= 12.10),
bzip2 (= 1.0.8-5+b2),
cmake (= 3.28.1-1),
cmake-data (= 3.28.1-1),
coreutils (= 9.4-3),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-13+rpi1),
cpp-13 (= 13.2.0-9+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.83),
debhelper (= 13.13),
debianutils (= 5.16),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.2+rpi1),
dpkg-dev (= 1.22.2+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
fontconfig-config (= 2.14.2-6),
fonts-dejavu-core (= 2.37-8),
fonts-dejavu-mono (= 2.37-8),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-9+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-13+rpi1),
gcc-12-base (= 12.3.0-13+rpi1),
gcc-13 (= 13.2.0-9+rpi1),
gcc-13-base (= 13.2.0-9+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
grep (= 3.11-4),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
help2man (= 1.49.3),
hicolor-icon-theme (= 0.17-2),
hostname (= 3.23+nmu2),
imagemagick (= 8:6.9.12.98+dfsg1-5+b1),
imagemagick-6-common (= 8:6.9.12.98+dfsg1-5),
imagemagick-6.q16 (= 8:6.9.12.98+dfsg1-5+b1),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-6),
libarchive-zip-perl (= 1.68-1),
libarchive13 (= 3.7.2-1),
libasan8 (= 13.2.0-9+rpi1),
libatomic1 (= 13.2.0-9+rpi1),
libattr1 (= 1:2.5.1-5),
libaudit-common (= 1:3.1.2-1),
libaudit1 (= 1:3.1.2-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.3-6),
libbrotli1 (= 1.1.0-2),
libbsd0 (= 0.11.8-1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.37-13+rpi1),
libc-dev-bin (= 2.37-13+rpi1),
libc6 (= 2.37-13+rpi1),
libc6-dev (= 2.37-13+rpi1),
libcap-ng0 (= 0.8.4-1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-9+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-4),
libcrypt1 (= 1:4.4.36-4),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl4 (= 8.5.0-2+rpi1),
libdav1d7 (= 1.3.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg2-4),
libde265-0 (= 1.0.15-1+rpi1),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.13),
libdeflate0 (= 1.19-1),
libdpkg-perl (= 1.22.2+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libexpat1 (= 2.5.0-2),
libffi8 (= 3.4.4-2),
libfftw3-double3 (= 3.3.10-1),
libfile-find-rule-perl (= 0.34-3),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libfontconfig1 (= 2.14.2-6),
libfreetype6 (= 2.13.2+dfsg-1),
libgcc-12-dev (= 12.3.0-13+rpi1),
libgcc-13-dev (= 13.2.0-9+rpi1),
libgcc-s1 (= 13.2.0-9+rpi1),
libgcrypt20 (= 1.10.3-2),
libgdbm-compat4 (= 1.23-5),
libgdbm6 (= 1.23-5),
libglib2.0-0 (= 2.78.3-2),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.3-1),
libgomp1 (= 13.2.0-9+rpi1),
libgpg-error0 (= 1.47-3),
libgssapi-krb5-2 (= 1.20.1-5),
libheif-plugin-dav1d (= 1.17.6-1),
libheif-plugin-libde265 (= 1.17.6-1),
libheif1 (= 1.17.6-1),
libhogweed6 (= 3.9.1-2),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libjbig0 (= 2.1-6.1),
libjpeg62-turbo (= 1:2.1.5-2),
libjsoncpp25 (= 1.9.5-6),
libk5crypto3 (= 1.20.1-5),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-5),
libkrb5support0 (= 1.20.1-5),
liblcms2-2 (= 2.14-2),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1+b1),
liblerc4 (= 4.0.0+ds-4),
liblocale-gettext-perl (= 1.07-6+b1),
liblqr-1-0 (= 0.4.2-2.1),
libltdl7 (= 2.4.7-7),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma5 (= 5.4.5-0.3),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmagickcore-6.q16-7 (= 8:6.9.12.98+dfsg1-5+b1),
libmagickwand-6.q16-7 (= 8:6.9.12.98+dfsg1-5+b1),
libmd0 (= 1.1.0-2),
libmount1 (= 2.39.3-6),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncursesw6 (= 6.4+20240113-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.59.0-1),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnumber-compare-perl (= 0.03-3),
libopenjp2-7 (= 2.5.0-2+b2),
libp11-kit0 (= 0.25.3-4),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.38 (= 5.38.2-3),
libpipeline1 (= 1.5.7-1),
libpng16-16 (= 1.6.40-3),
libproc2-0 (= 2:4.0.4-4),
libpsl5 (= 0.21.2-1+b1),
libraw23 (= 0.21.1-7+rpi1),
librhash0 (= 1.4.3-3),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-4),
libsasl2-modules-db (= 2.1.28+dfsg1-4),
libseccomp2 (= 2.5.4-2+rpi1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsharpyuv0 (= 1.3.2-0.3),
libsimde-dev (= 0.7.6-1),
libsmartcols1 (= 2.39.3-6),
libssh2-1 (= 1.11.0-4),
libssl3 (= 3.1.4-2),
libstdc++-13-dev (= 13.2.0-9+rpi1),
libstdc++6 (= 13.2.0-9+rpi1),
libsub-override-perl (= 0.10-1),
libsystemd0 (= 254.5-1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtext-glob-perl (= 0.11-3),
libtiff6 (= 4.5.1+git230720-4),
libtinfo6 (= 6.4+20240113-1),
libtirpc-common (= 1.3.4+ds-1),
libtirpc-dev (= 1.3.4+ds-1),
libtirpc3 (= 1.3.4+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-9+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-6),
libuv1 (= 1.46.0-3+rpi1),
libwebp7 (= 1.3.2-0.3),
libwebpdemux2 (= 1.3.2-0.3),
libwebpmux3 (= 1.3.2-0.3),
libx11-6 (= 2:1.8.7-1),
libx11-data (= 2:1.8.7-1),
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-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1+b1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-3),
mawk (= 1.3.4.20231126-1),
ncurses-base (= 6.4+20240113-1),
ncurses-bin (= 6.4+20240113-1),
patch (= 2.7.6-7),
perl (= 5.38.2-3),
perl-base (= 5.38.2-3),
perl-modules-5.38 (= 5.38.2-3),
po-debconf (= 1.0.21+nmu1),
procps (= 2:4.0.4-4),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-2),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-5),
tar (= 1.35+dfsg-3),
usr-is-merged (= 38),
usrmerge (= 38),
util-linux (= 2.39.3-6),
xz-utils (= 5.4.5-0.3),
zlib1g (= 1:1.3.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1707347751"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
hhsuite-dbgsym_3.3.0+ds-8+b1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 16990212 bytes: control archive=1744 bytes.
1381 bytes, 12 lines control
2737 bytes, 26 lines md5sums
Package: hhsuite-dbgsym
Source: hhsuite (3.3.0+ds-8)
Version: 3.3.0+ds-8+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 17570
Depends: hhsuite (= 3.3.0+ds-8+b1)
Section: debug
Priority: optional
Description: debug symbols for hhsuite
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drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 616136 2024-02-07 23:15 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/hhsuite.debug
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/share/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-02-07 23:15 ./usr/share/doc/hhsuite-dbgsym -> hhsuite
hhsuite_3.3.0+ds-8+b1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 10241928 bytes: control archive=2852 bytes.
1505 bytes, 30 lines control
4393 bytes, 66 lines md5sums
Package: hhsuite
Source: hhsuite (3.3.0+ds-8)
Version: 3.3.0+ds-8+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 76674
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 13.1), perl:any, hhsuite-data (= 3.3.0+ds-8), python3
Conflicts: ffindex
Built-Using: simde (= 0.7.6-1)
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 2024-02-07 23:15 ./
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/bin/
-rwxr-xr-x root/root 38548 2024-02-07 23:15 ./usr/bin/a3m_database_extract
-rwxr-xr-x root/root 42644 2024-02-07 23:15 ./usr/bin/a3m_database_filter
-rwxr-xr-x root/root 38548 2024-02-07 23:15 ./usr/bin/a3m_database_reduce
-rwxr-xr-x root/root 38548 2024-02-07 23:15 ./usr/bin/a3m_extract
-rwxr-xr-x root/root 38548 2024-02-07 23:15 ./usr/bin/a3m_reduce
-rwxr-xr-x root/root 22192 2024-02-07 23:15 ./usr/bin/ffindex_apply
-rwxr-xr-x root/root 18128 2024-02-07 23:15 ./usr/bin/ffindex_build
-rwxr-xr-x root/root 18064 2024-02-07 23:15 ./usr/bin/ffindex_from_fasta
-rwxr-xr-x root/root 18016 2024-02-07 23:15 ./usr/bin/ffindex_from_fasta_with_split
-rwxr-xr-x root/root 18048 2024-02-07 23:15 ./usr/bin/ffindex_get
-rwxr-xr-x root/root 18096 2024-02-07 23:15 ./usr/bin/ffindex_modify
-rwxr-xr-x root/root 18016 2024-02-07 23:15 ./usr/bin/ffindex_order
-rwxr-xr-x root/root 18016 2024-02-07 23:15 ./usr/bin/ffindex_reduce
-rwxr-xr-x root/root 18016 2024-02-07 23:15 ./usr/bin/ffindex_unpack
-rwxr-xr-x root/root 7992992 2024-02-07 23:15 ./usr/bin/hhalign
-rwxr-xr-x root/root 8005280 2024-02-07 23:15 ./usr/bin/hhalign_omp
-rwxr-xr-x root/root 7956128 2024-02-07 23:15 ./usr/bin/hhblits
-rwxr-xr-x root/root 7964320 2024-02-07 23:15 ./usr/bin/hhblits_ca3m
-rwxr-xr-x root/root 7968416 2024-02-07 23:15 ./usr/bin/hhblits_omp
-rwxr-xr-x root/root 7526044 2024-02-07 23:15 ./usr/bin/hhconsensus
-rwxr-xr-x root/root 272024 2024-02-07 23:15 ./usr/bin/hhfilter
-rwxr-xr-x root/root 7513756 2024-02-07 23:15 ./usr/bin/hhmake
-rwxr-xr-x root/root 7988896 2024-02-07 23:15 ./usr/bin/hhsearch
-rwxr-xr-x root/root 7997088 2024-02-07 23:15 ./usr/bin/hhsearch_omp
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/lib/
lrwxrwxrwx root/root 0 2024-02-07 23:15 ./usr/lib/hh -> hhsuite
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/lib/hhsuite/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./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 2024-02-07 23:15 ./usr/lib/hhsuite/scripts -> ../../share/hhsuite/scripts
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/libexec/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/libexec/hhsuite/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/libexec/hhsuite/bin/
-rwxr-xr-x root/root 6190760 2024-02-07 23:15 ./usr/libexec/hhsuite/bin/cstranslate
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/share/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./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 219 2024-02-07 23:15 ./usr/share/doc/hhsuite/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1841 2024-02-07 23:15 ./usr/share/doc/hhsuite/changelog.Debian.gz
-rw-r--r-- root/root 20399 2023-08-13 08:47 ./usr/share/doc/hhsuite/copyright
drwxr-xr-x root/root 0 2024-02-07 23:15 ./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 2024-02-07 23:15 ./usr/share/hhsuite/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./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 2024-02-07 23:15 ./usr/share/hhsuite/scripts/a3m.py
-rwxr-xr-x root/root 31681 2024-02-07 23:15 ./usr/share/hhsuite/scripts/addss.pl
-rwxr-xr-x root/root 438 2024-02-07 23:15 ./usr/share/hhsuite/scripts/check_a3m.py
-rwxr-xr-x root/root 28735 2024-02-07 23:15 ./usr/share/hhsuite/scripts/cif2fasta.py
-rwxr-xr-x root/root 4654 2024-02-07 23:15 ./usr/share/hhsuite/scripts/create_profile_from_hhm.pl
-rwxr-xr-x root/root 6815 2024-02-07 23:15 ./usr/share/hhsuite/scripts/create_profile_from_hmmer.pl
-rwxr-xr-x root/root 2081 2024-02-07 23:15 ./usr/share/hhsuite/scripts/ffindex.py
-rwxr-xr-x root/root 446 2024-02-07 23:15 ./usr/share/hhsuite/scripts/get_a3m_size.py
-rwxr-xr-x root/root 7179 2024-02-07 23:15 ./usr/share/hhsuite/scripts/hh_reader.py
-rwxr-xr-x root/root 48079 2024-02-07 23:15 ./usr/share/hhsuite/scripts/hhmakemodel.pl
-rwxr-xr-x root/root 87343 2024-02-07 23:15 ./usr/share/hhsuite/scripts/hhmakemodel.py
-rwxr-xr-x root/root 16961 2024-02-07 23:15 ./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 2024-02-07 23:15 ./usr/share/hhsuite/scripts/multithread.pl
-rwxr-xr-x root/root 40490 2024-02-07 23:15 ./usr/share/hhsuite/scripts/pdb2fasta.pl
-rwxr-xr-x root/root 13183 2024-02-07 23:15 ./usr/share/hhsuite/scripts/pdbfilter.pl
-rwxr-xr-x root/root 8648 2024-02-07 23:15 ./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 2024-02-07 23:15 ./usr/share/hhsuite/scripts/renumberpdb.pl
-rwxr-xr-x root/root 3651 2024-02-07 23:15 ./usr/share/hhsuite/scripts/splitfasta.pl
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/share/man/
drwxr-xr-x root/root 0 2024-02-07 23:15 ./usr/share/man/man1/
-rw-r--r-- root/root 3090 2024-02-07 23:15 ./usr/share/man/man1/hhalign.1.gz
-rw-r--r-- root/root 4143 2024-02-07 23:15 ./usr/share/man/man1/hhblits.1.gz
-rw-r--r-- root/root 4153 2024-02-07 23:15 ./usr/share/man/man1/hhblits_omp.1.gz
-rw-r--r-- root/root 1031 2024-02-07 23:15 ./usr/share/man/man1/hhconsensus.1.gz
-rw-r--r-- root/root 1023 2024-02-07 23:15 ./usr/share/man/man1/hhfilter.1.gz
-rw-r--r-- root/root 1658 2024-02-07 23:15 ./usr/share/man/man1/hhmake.1.gz
-rw-r--r-- root/root 3358 2024-02-07 23:15 ./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: 569496
Build-Time: 169
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 65
Job: hhsuite_3.3.0+ds-8
Machine Architecture: arm64
Package: hhsuite
Package-Time: 243
Source-Version: 3.3.0+ds-8
Space: 569496
Status: successful
Version: 3.3.0+ds-8+b1
--------------------------------------------------------------------------------
Finished at 2024-02-07T23:18:40Z
Build needed 00:04:03, 569496k disk space