hhsuite →
3.3.0+ds-8 →
armhf → 2023-09-20 05:13:17
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| hhsuite 3.3.0+ds-8 (armhf) Wed, 20 Sep 2023 04:38:45 +0000 |
+==============================================================================+
Package: hhsuite
Version: 3.3.0+ds-8
Source Version: 3.3.0+ds-8
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-bd4f4c57-80bb-4f06-ad7f-9eda0258dda2' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| 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 [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.7 MB]
Fetched 28.7 MB in 31s (915 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/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 (4454 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hhsuite-FHBqrN/hhsuite-3.3.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hhsuite-FHBqrN' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-uLPJhv/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-uLPJhv/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-uLPJhv/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Packages [435 B]
Fetched 2111 B in 1s (2936 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils sgml-base
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 49 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (15.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11771 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man
Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, cmake, imagemagick, help2man
dpkg-deb: building package 'sbuild-build-depends-hhsuite-dummy' in '/<<BUILDDIR>>/resolver-uLPJhv/apt_archive/sbuild-build-depends-hhsuite-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-hhsuite-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Sources [517 B]
Get:5 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ Packages [600 B]
Fetched 2450 B in 1s (3465 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install hhsuite build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file
fontconfig-config fonts-noto-core fonts-noto-mono gettext gettext-base
groff-base help2man hicolor-icon-theme imagemagick imagemagick-6-common
imagemagick-6.q16 intltool-debian libarchive-zip-perl libarchive13 libblkid1
libbrotli1 libbsd0 libcurl4 libdav1d6 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 liblocale-gettext-perl
liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6
libmagickwand-6.q16-6 libmount1 libnghttp2-14 libopenjp2-7 libpipeline1
libpng16-16 libproc2-0 libpsl5 librhash0 librtmp1 libsimde-dev libsmartcols1
libssh2-1 libsub-override-perl libtiff6 libtool libuchardet0 libuuid1 libuv1
libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1
libxdmcp6 libxext6 libxml2 m4 man-db mount po-debconf procps util-linux
util-linux-extra
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-doc autotrace cups-bsd | lpr | lprng curl
enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer
povray radiance sane-utils texlive-base-bin transfig ufraw-batch xdg-utils
lrzip libfftw3-bin libfftw3-dev low-memory-monitor libheif-plugin-rav1e
libheif-plugin-svtenc liblcms2-utils libmagickcore-6.q16-6-extra
cryptsetup-bin libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser nfs-common libmail-box-perl dosfstools kbd
util-linux-locales
Recommended packages:
curl | wget | lynx libmagickcore-6.q16-6-extra ghostscript netpbm
ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libheif-plugin-aomenc libheif-plugin-x265 gsfonts publicsuffix
libltdl-dev uuid-runtime 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-noto-core fonts-noto-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
libdav1d6 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
liblocale-gettext-perl liblqr-1-0 libltdl7 libmagic-mgc libmagic1
libmagickcore-6.q16-6 libmagickwand-6.q16-6 libnghttp2-14 libopenjp2-7
libpipeline1 libpng16-16 libproc2-0 libpsl5 librhash0 librtmp1 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-hhsuite-dummy
The following packages will be upgraded:
bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 mount util-linux
util-linux-extra
8 upgraded, 86 newly installed, 0 to remove and 41 not upgraded.
Need to get 54.5 MB of archives.
After this operation, 193 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-uLPJhv/apt_archive ./ sbuild-build-depends-hhsuite-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-1 [85.9 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-1 [143 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-1 [166 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-1 [101 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf util-linux-extra armhf 2.39.2-1 [136 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-1 [1107 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf liblocale-gettext-perl armhf 1.07-5 [14.9 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-1 [132 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libfftw3-double3 armhf 3.3.10-1 [325 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-1 [258 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [366 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf fonts-noto-mono all 20201225-2 [398 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf fonts-noto-core all 20201225-2 [12.2 MB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.14.2-5 [314 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.14.2-5 [367 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libdav1d6 armhf 1.0.0-2+rpi1 [205 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-dav1d armhf 1.16.2-2 [8864 B]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libde265-0 armhf 1.0.11-1+rpi1 [137 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libheif-plugin-libde265 armhf 1.16.2-2 [11.8 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libheif1 armhf 1.16.2-2 [188 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf liblcms2-2 armhf 2.14-2 [124 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0 armhf 2.74.6-1 [1203 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.1 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libltdl7 armhf 2.4.7-7 [390 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libopenjp2-7 armhf 2.5.0-2 [164 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf liblerc4 armhf 4.0.0+ds-3 [133 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libwebp7 armhf 1.2.4-0.2 [242 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libtiff6 armhf 4.5.1+git230720-1 [298 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libwebpdemux2 armhf 1.2.4-0.2 [98.4 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libwebpmux3 armhf 1.2.4-0.2 [106 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.6-1 [323 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.6-1 [726 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf imagemagick-6-common all 8:6.9.11.60+dfsg-1.6 [165 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libmagickcore-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6 [1596 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libmagickwand-6.q16-6 armhf 8:6.9.11.60+dfsg-1.6 [385 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-1 [27.7 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.22.4-10 [774 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-1 [80.5 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libproc2-0 armhf 2:4.0.3-1 [54.2 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf procps armhf 2:4.0.3-1 [731 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-12 [156 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-3 [256 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libarchive13 armhf 3.6.2-1 [293 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.52.0-1 [60.6 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 7.88.1-10+rpi1 [343 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libjsoncpp25 armhf 1.9.5-6 [64.7 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libuv1 armhf 1.44.2-1+rpi1 [125 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf cmake-data all 3.27.4-1 [2103 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf cmake armhf 3.27.4-1 [7752 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-12 [1201 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf help2man armhf 1.49.3 [198 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.6 [339 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf imagemagick armhf 8:6.9.11.60+dfsg-1.6 [122 kB]
Get:94 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 help2man (1.49.3) ...
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 (1.22.4-10) ...
Setting up libcurl4:armhf (7.88.1-10+rpi1) ...
Setting up libx11-6:armhf (2:1.8.6-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.11.2-3) ...
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Setting up cmake (3.27.4-1) ...
Setting up debhelper (13.11.6) ...
Setting up libheif-plugin-dav1d:armhf (1.16.2-2) ...
Setting up libheif-plugin-libde265:armhf (1.16.2-2) ...
Setting up libheif1:armhf (1.16.2-2) ...
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Setting up libfontconfig1:armhf (2.14.2-5) ...
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
Setting up libmagickcore-6.q16-6:armhf (8:6.9.11.60+dfsg-1.6) ...
Setting up libmagickwand-6.q16-6:armhf (8:6.9.11.60+dfsg-1.6) ...
Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.6) ...
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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
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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-hhsuite-dummy (0.invalid.0) ...
Setting up imagemagick (8:6.9.11.60+dfsg-1.6) ...
Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.6.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_12.4+rpi1+deb12u1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-1 bsdutils_1:2.39.2-1 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.27.4-1 cmake-data_3.27.4-1 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.6 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.31-1.2 file_1:5.45-2 findutils_4.9.0-4 fontconfig-config_2.14.2-5 fonts-noto-core_20201225-2 fonts-noto-mono_20201225-2 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
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 /<<BUILDDIR>>/hhsuite-3.3.0+ds
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 disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-bd4f4c57-80bb-4f06-ad7f-9eda0258dda2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package hhsuite
dpkg-buildpackage: info: source version 3.3.0+ds-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
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 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Compiler is GNU
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 (19.4s)
-- Generating done (0.6s)
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: /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild
make[1]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
dh_auto_build --builddirectory mybuild
cd mybuild && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
/usr/bin/cmake -S/<<BUILDDIR>>/hhsuite-3.3.0+ds -B/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/CMakeFiles /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/hhsuite-3.3.0+ds /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/hhsuite-3.3.0+ds /<<BUILDDIR>>/hhsuite-3.3.0+ds/data /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/data /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && /<<BUILDDIR>>/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h
/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c: In function 'ffindex_index_parse':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/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=]
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| ~~^ ~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1
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[ 11%] Generating ../generated/cs219.lib.h
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && mkdir -p /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && mv -f /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/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
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs/aa.cc
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_compress.cpp
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c
/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/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
/<<BUILDDIR>>/hhsuite-3.3.0+ds/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
[ 15%] Linking C executable ffindex_apply
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make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
504 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_compress.h:11,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_compress.cpp:8:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
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[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c
[ 30%] Linking CXX static library libA3M_COMPRESS.a
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[ 31%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c
[ 32%] Linking C executable ffindex_order
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[ 33%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/hhsuite-3.3.0+ds /<<BUILDDIR>>/hhsuite-3.3.0+ds/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake "--color="
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[ 35%] Linking C executable ffindex_from_fasta_with_split
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/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a
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[ 37%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp
[ 38%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc
[ 39%] Linking CXX executable a3m_extract
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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[ 39%] Built target a3m_extract
make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/hhsuite-3.3.0+ds /<<BUILDDIR>>/hhsuite-3.3.0+ds/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake "--color="
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make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build
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[ 40%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp
[ 41%] Linking CXX executable a3m_reduce
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/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=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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[ 41%] Built target a3m_reduce
make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend
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[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhmatrices.cpp
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhit.cpp
[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o
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[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalign.cpp
[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhitlist.cpp
[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp
[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhutil.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhit.h:14,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhitlist.h:16,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhitlist.cpp:9:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Hit>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]',
inlined from 'void HitList::PrintMatrices(HMM*, std::stringstream&, bool, size_t, const float (*)[20])' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhitlist.cpp:591:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/util.cpp
[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.cpp
[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp
[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhmm.cpp
[ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o
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[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=]
1797 | sprintf(details, "The alingment %s does not contain any sequences.",
| ^~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.h:6,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.cpp:8:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:14:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o
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[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o
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[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o
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[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp
[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhdatabase.cpp
[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp
[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd/simd.h:9,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/util.h:23,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhmm.h:8,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.h:17,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.cpp:8:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Distance = int; _Tp = pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.h:11:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::pair<double, int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from '_ZN9Prefilter12prefilter_dbEP3HMMP4HashI3HitEiiiiiddiiiPA20_KfRSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaISH_EESK_._omp_fn.1' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.cpp:531:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhfunc.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/util.h:20,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhmm.h:8,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhmmsimd.h:5,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbirunner.h:4,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Hit>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]',
inlined from 'void ViterbiConsumerThread::align(int, int, float, char)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:67:23:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Hit; _Alloc = std::allocator<Hit>]',
inlined from 'void ViterbiRunner::merge_thread_results(std::vector<Hit>&, std::vector<HHEntry*>&, std::map<std::__cxx11::basic_string<char>, std::vector<Viterbi::BacktraceResult> >&, std::vector<ViterbiConsumerThread*>&, int, float)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/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 /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:173:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1625 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]',
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]' at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = comparePair]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void Prefilter::prefilter_db(HMM*, Hash<Hit>*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&, std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<double, int>*, vector<pair<double, int> > >; _Compare = comparePair]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'void Prefilter::prefilter_db(HMM*, Hash<Hit>*, int, int, int, int, int, double, double, int, int, int, const float (*)[20], std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&, std::vector<std::pair<int, std::__cxx11::basic_string<char> > >&)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.cpp:536:12:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In 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 /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp:259:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 79%] Linking CXX static library libHH_OBJECTS.a
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds/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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/hhsuite-3.3.0+ds /<<BUILDDIR>>/hhsuite-3.3.0+ds/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
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make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 93%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp
[ 94%] Linking CXX executable hhconsensus
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 94%] Built target hhconsensus
make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/hhsuite-3.3.0+ds /<<BUILDDIR>>/hhsuite-3.3.0+ds/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 95%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhsearch.h:34,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17,
inlined from 'int main(int, const char**)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/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 /<<BUILDDIR>>/hhsuite-3.3.0+ds/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=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/hhsuite-3.3.0+ds /<<BUILDDIR>>/hhsuite-3.3.0+ds/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 97%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simde -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/simd -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src -I/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhsearch.h:34,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17,
inlined from 'int main(int, const char**)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/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 /<<BUILDDIR>>/hhsuite-3.3.0+ds/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=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 98%] Built target hhsearch_omp
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhsearch.h:34,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17,
inlined from 'int main(int, const char**)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/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 /<<BUILDDIR>>/hhsuite-3.3.0+ds/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=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)':
/<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base);
| ^~~~~~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/12/cstdio:42,
from /usr/include/c++/12/ext/string_conversions.h:43,
from /usr/include/c++/12/bits/basic_string.h:3960,
from /usr/include/c++/12/string:53,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/fstream:38,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits.h:11,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8:
In function 'int snprintf(char*, size_t, const char*, ...)',
inlined from 'void OutputFFIndex::close()' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15,
inlined from 'int main(int, const char**)' at /<<BUILDDIR>>/hhsuite-3.3.0+ds/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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 99%] Built target hhalign_omp
[100%] Linking CXX executable hhblits_ca3m
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/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=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[100%] Built target hhblits_ca3m
[100%] Linking CXX executable cstranslate
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[100%] Built target cstranslate
make[3]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/CMakeFiles 0
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make[1]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && PATH=$PATH:/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src:/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh
- 05:05:28.668 INFO: query.a3m is in A2M, A3M or FASTA format
- 05:05:35.231 INFO: Alternative alignment: 0
- 05:05:35.749 INFO: 1 alignments done
- 05:05:36.108 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 Sep 20 05:05:37 2023
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 4872 0
query.a3m 0 32666 25 0
query.a3m 0 32666 924 0
Reading context library for pseudocounts from internal ...
Reading abstract state alphabet from internal ...
Processing entry: query.a3m
Adding cs-pseudocounts (admix=0.30) ...
- 05:05:57.319 INFO: Searching 1 column state sequences.
- 05:05:57.923 INFO: query.a3m is in A2M, A3M or FASTA format
- 05:05:58.164 INFO: Iteration 1
- 05:06:03.904 INFO: Prefiltering database
- 05:06:09.600 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 05:06:09.639 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 05:06:09.639 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 05:06:09.639 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 05:06:10.119 INFO: Alternative alignment: 0
- 05:06:10.623 INFO: 1 alignments done
- 05:06:10.623 INFO: Alternative alignment: 1
- 05:06:11.125 INFO: 1 alignments done
- 05:06:11.126 INFO: Alternative alignment: 2
- 05:06:11.126 INFO: Alternative alignment: 3
- 05:06:17.705 INFO: Premerge done
- 05:06:17.707 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 05:06:18.205 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 Sep 20 05:06:18 2023
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)
- 05:06:18.434 INFO: Searching 1 column state sequences.
- 05:06:18.946 INFO: Thread 0 query.a3m
- 05:06:19.067 INFO: query.a3m is in A2M, A3M or FASTA format
- 05:06:19.309 INFO: Iteration 1
- 05:06:30.332 INFO: Prefiltering database
- 05:06:41.434 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 05:06:41.471 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 05:06:41.471 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 05:06:41.472 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 05:06:41.713 INFO: Alternative alignment: 0
- 05:06:42.218 INFO: 1 alignments done
- 05:06:42.219 INFO: Alternative alignment: 1
- 05:06:42.718 INFO: 1 alignments done
- 05:06:42.719 INFO: Alternative alignment: 2
- 05:06:42.719 INFO: Alternative alignment: 3
- 05:06:54.333 INFO: Premerge done
- 05:06:54.334 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 05:06:54.723 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
- 05:06:55.615 INFO: query.a3m is in A2M, A3M or FASTA format
- 05:06:55.855 INFO: Searching 1 database HHMs without prefiltering
- 05:06:55.855 INFO: Iteration 1
- 05:07:01.599 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 05:07:02.080 INFO: Alternative alignment: 0
- 05:07:02.582 INFO: 1 alignments done
- 05:07:02.582 INFO: Alternative alignment: 1
- 05:07:03.083 INFO: 1 alignments done
- 05:07:03.085 INFO: Alternative alignment: 2
- 05:07:03.085 INFO: Alternative alignment: 3
- 05:07:09.742 INFO: Premerge done
- 05:07:09.744 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 05:07:10.241 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 Sep 20 05:07:10 2023
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)
- 05:07:10.979 INFO: Thread 0 query.a3m
- 05:07:11.102 INFO: query.a3m is in A2M, A3M or FASTA format
- 05:07:11.343 INFO: Searching 1 database HHMs without prefiltering
- 05:07:11.345 INFO: Iteration 1
- 05:07:22.430 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 05:07:22.671 INFO: Alternative alignment: 0
- 05:07:23.177 INFO: 1 alignments done
- 05:07:23.178 INFO: Alternative alignment: 1
- 05:07:23.678 INFO: 1 alignments done
- 05:07:23.679 INFO: Alternative alignment: 2
- 05:07:23.679 INFO: Alternative alignment: 3
- 05:07:35.392 INFO: Premerge done
- 05:07:35.394 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 05:07:35.791 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
make[1]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
mkdir -p /<<BUILDDIR>>/hhsuite-3.3.0+ds/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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
/usr/bin/cmake -S/<<BUILDDIR>>/hhsuite-3.3.0+ds -B/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_reduce
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_apply
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_build
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_get
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_modify
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_unpack
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_order
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/ffindex_from_fasta_with_split
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.crf
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/data/context_data.lib
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/data/cs219.lib
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.phr
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.pin
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/data/do_not_delete.psq
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhmake
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhfilter
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhconsensus
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_extract
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_reduce
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_reduce
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_extract
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/a3m_database_filter
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/cstranslate
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_omp
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhsearch_omp
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhalign_omp
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/bin/hhblits_ca3m
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/a3m.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/addss.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/Align.pm
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/check_a3m.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/cif2fasta.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hhm.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/create_profile_from_hmmer.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/ffindex.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/get_a3m_size.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hh_reader.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhmakemodel.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/HHPaths.pm
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/hhsuitedb.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/mergeali.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/multithread.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdb2fasta.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/pdbfilter.py
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/reformat.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl
-- Installing: /<<BUILDDIR>>/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl
make[2]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
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 '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
dh_fixperms
chmod -x debian/hhsuite/usr/share/hhsuite/scripts/*.pm
make[1]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhmake contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_ca3m contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhconsensus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_extract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhfilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhblits_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_reduce contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/hhsearch_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/hhsuite/usr/bin/hhmake debian/hhsuite/usr/bin/hhalign_omp debian/hhsuite/usr/bin/a3m_database_extract debian/hhsuite/usr/bin/hhblits_ca3m debian/hhsuite/usr/bin/ffindex_from_fasta_with_split debian/hhsuite/usr/bin/hhblits debian/hhsuite/usr/bin/ffindex_from_fasta debian/hhsuite/usr/bin/a3m_database_filter debian/hhsuite/usr/bin/ffindex_unpack debian/hhsuite/usr/bin/ffindex_build debian/hhsuite/usr/bin/hhsearch debian/hhsuite/usr/bin/ffindex_modify debian/hhsuite/usr/bin/hhconsensus debian/hhsuite/usr/bin/a3m_extract debian/hhsuite/usr/bin/ffindex_order debian/hhsuite/usr/bin/ffindex_reduce debian/hhsuite/usr/bin/hhfilter debian/hhsuite/usr/bin/hhblits_omp debian/hhsuite/usr/bin/a3m_database_reduce debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate debian/hhsuite/usr/bin/ffindex_apply debian/hhsuite/usr/bin/a3m_reduce debian/hhsuite/usr/bin/hhalign debian/hhsuite/usr/bin/ffindex_get debian/hhsuite/usr/bin/hhsearch_omp were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.6-1), "
make[1]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_armhf.deb'.
dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_armhf.deb'.
dpkg-genbuildinfo --build=any -O../hhsuite_3.3.0+ds-8_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../hhsuite_3.3.0+ds-8_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-09-20T05:13:00Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
hhsuite_3.3.0+ds-8_armhf.changes:
---------------------------------
Format: 1.8
Date: Sun, 13 Aug 2023 10:47:11 +0200
Source: hhsuite
Binary: hhsuite hhsuite-dbgsym
Architecture: armhf
Version: 3.3.0+ds-8
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
Closes: 1037689
Changes:
hhsuite (3.3.0+ds-8) unstable; urgency=medium
.
* Team upload.
* gcc-13.patch: new: fix ftbfs with gcc 13. (Closes: #1037689)
* d/control: declare compliance to standards version 4.6.2.
Checksums-Sha1:
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b87e035692872ff3ad1175bb57b87707d6e7cf76 7066 hhsuite_3.3.0+ds-8_armhf.buildinfo
b6856a8d1e992c7f7546748c06cd353a04e62992 10233020 hhsuite_3.3.0+ds-8_armhf.deb
Checksums-Sha256:
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63829df38e87382ef0065d518599ae1383b52b8dca38b0b796f524e4fdc3ac09 7066 hhsuite_3.3.0+ds-8_armhf.buildinfo
de4d19d5bc0827f7615f539c67aec22e62e8417d87ac1c560167cc3aecc8143b 10233020 hhsuite_3.3.0+ds-8_armhf.deb
Files:
2a00565fb46f9ccef94e5dab9299be90 17643420 debug optional hhsuite-dbgsym_3.3.0+ds-8_armhf.deb
9182dc32a6dde1e0ae2b185acf4070ea 7066 science optional hhsuite_3.3.0+ds-8_armhf.buildinfo
00a98ab95f2fd563854fc447ca6677be 10233020 science optional hhsuite_3.3.0+ds-8_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
hhsuite-dbgsym_3.3.0+ds-8_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 17643420 bytes: control archive=1732 bytes.
1362 bytes, 12 lines control
2737 bytes, 26 lines md5sums
Package: hhsuite-dbgsym
Source: hhsuite
Version: 3.3.0+ds-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18262
Depends: hhsuite (= 3.3.0+ds-8)
Section: debug
Priority: optional
Description: debug symbols for hhsuite
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drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/debug/.dwz/
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-rw-r--r-- root/root 618236 2023-08-13 08:47 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/hhsuite.debug
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lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/share/doc/hhsuite-dbgsym -> hhsuite
hhsuite_3.3.0+ds-8_armhf.deb
----------------------------
new Debian package, version 2.0.
size 10233020 bytes: control archive=2824 bytes.
1471 bytes, 29 lines control
4311 bytes, 65 lines md5sums
Package: hhsuite
Version: 3.3.0+ds-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 76533
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 11), 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 2023-08-13 08:47 ./
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/bin/
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-rwxr-xr-x root/root 42644 2023-08-13 08:47 ./usr/bin/a3m_database_filter
-rwxr-xr-x root/root 38548 2023-08-13 08:47 ./usr/bin/a3m_database_reduce
-rwxr-xr-x root/root 38548 2023-08-13 08:47 ./usr/bin/a3m_extract
-rwxr-xr-x root/root 38548 2023-08-13 08:47 ./usr/bin/a3m_reduce
-rwxr-xr-x root/root 22192 2023-08-13 08:47 ./usr/bin/ffindex_apply
-rwxr-xr-x root/root 18128 2023-08-13 08:47 ./usr/bin/ffindex_build
-rwxr-xr-x root/root 18064 2023-08-13 08:47 ./usr/bin/ffindex_from_fasta
-rwxr-xr-x root/root 18016 2023-08-13 08:47 ./usr/bin/ffindex_from_fasta_with_split
-rwxr-xr-x root/root 18048 2023-08-13 08:47 ./usr/bin/ffindex_get
-rwxr-xr-x root/root 18096 2023-08-13 08:47 ./usr/bin/ffindex_modify
-rwxr-xr-x root/root 18016 2023-08-13 08:47 ./usr/bin/ffindex_order
-rwxr-xr-x root/root 18016 2023-08-13 08:47 ./usr/bin/ffindex_reduce
-rwxr-xr-x root/root 18016 2023-08-13 08:47 ./usr/bin/ffindex_unpack
-rwxr-xr-x root/root 7976608 2023-08-13 08:47 ./usr/bin/hhalign
-rwxr-xr-x root/root 7984800 2023-08-13 08:47 ./usr/bin/hhalign_omp
-rwxr-xr-x root/root 7939744 2023-08-13 08:47 ./usr/bin/hhblits
-rwxr-xr-x root/root 7943840 2023-08-13 08:47 ./usr/bin/hhblits_ca3m
-rwxr-xr-x root/root 7947936 2023-08-13 08:47 ./usr/bin/hhblits_omp
-rwxr-xr-x root/root 7521948 2023-08-13 08:47 ./usr/bin/hhconsensus
-rwxr-xr-x root/root 267928 2023-08-13 08:47 ./usr/bin/hhfilter
-rwxr-xr-x root/root 7509660 2023-08-13 08:47 ./usr/bin/hhmake
-rwxr-xr-x root/root 7968416 2023-08-13 08:47 ./usr/bin/hhsearch
-rwxr-xr-x root/root 7976608 2023-08-13 08:47 ./usr/bin/hhsearch_omp
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/
lrwxrwxrwx root/root 0 2023-08-13 08:47 ./usr/lib/hh -> hhsuite
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/lib/hhsuite/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./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 2023-08-13 08:47 ./usr/lib/hhsuite/scripts -> ../../share/hhsuite/scripts
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/libexec/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/libexec/hhsuite/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/libexec/hhsuite/bin/
-rwxr-xr-x root/root 6194856 2023-08-13 08:47 ./usr/libexec/hhsuite/bin/cstranslate
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./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 1841 2023-08-13 08:47 ./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 2023-08-13 08:47 ./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 2023-08-13 08:47 ./usr/share/hhsuite/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./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 2023-08-13 08:47 ./usr/share/hhsuite/scripts/a3m.py
-rwxr-xr-x root/root 31681 2023-08-13 08:47 ./usr/share/hhsuite/scripts/addss.pl
-rwxr-xr-x root/root 438 2023-08-13 08:47 ./usr/share/hhsuite/scripts/check_a3m.py
-rwxr-xr-x root/root 28735 2023-08-13 08:47 ./usr/share/hhsuite/scripts/cif2fasta.py
-rwxr-xr-x root/root 4654 2023-08-13 08:47 ./usr/share/hhsuite/scripts/create_profile_from_hhm.pl
-rwxr-xr-x root/root 6815 2023-08-13 08:47 ./usr/share/hhsuite/scripts/create_profile_from_hmmer.pl
-rwxr-xr-x root/root 2081 2023-08-13 08:47 ./usr/share/hhsuite/scripts/ffindex.py
-rwxr-xr-x root/root 446 2023-08-13 08:47 ./usr/share/hhsuite/scripts/get_a3m_size.py
-rwxr-xr-x root/root 7179 2023-08-13 08:47 ./usr/share/hhsuite/scripts/hh_reader.py
-rwxr-xr-x root/root 48079 2023-08-13 08:47 ./usr/share/hhsuite/scripts/hhmakemodel.pl
-rwxr-xr-x root/root 87343 2023-08-13 08:47 ./usr/share/hhsuite/scripts/hhmakemodel.py
-rwxr-xr-x root/root 16961 2023-08-13 08:47 ./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 2023-08-13 08:47 ./usr/share/hhsuite/scripts/multithread.pl
-rwxr-xr-x root/root 40490 2023-08-13 08:47 ./usr/share/hhsuite/scripts/pdb2fasta.pl
-rwxr-xr-x root/root 13183 2023-08-13 08:47 ./usr/share/hhsuite/scripts/pdbfilter.pl
-rwxr-xr-x root/root 8648 2023-08-13 08:47 ./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 2023-08-13 08:47 ./usr/share/hhsuite/scripts/renumberpdb.pl
-rwxr-xr-x root/root 3651 2023-08-13 08:47 ./usr/share/hhsuite/scripts/splitfasta.pl
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/man/
drwxr-xr-x root/root 0 2023-08-13 08:47 ./usr/share/man/man1/
-rw-r--r-- root/root 3088 2023-08-13 08:47 ./usr/share/man/man1/hhalign.1.gz
-rw-r--r-- root/root 4141 2023-08-13 08:47 ./usr/share/man/man1/hhblits.1.gz
-rw-r--r-- root/root 4151 2023-08-13 08:47 ./usr/share/man/man1/hhblits_omp.1.gz
-rw-r--r-- root/root 1029 2023-08-13 08:47 ./usr/share/man/man1/hhconsensus.1.gz
-rw-r--r-- root/root 1021 2023-08-13 08:47 ./usr/share/man/man1/hhfilter.1.gz
-rw-r--r-- root/root 1656 2023-08-13 08:47 ./usr/share/man/man1/hhmake.1.gz
-rw-r--r-- root/root 3357 2023-08-13 08:47 ./usr/share/man/man1/hhsearch.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 575220
Build-Time: 1281
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 713
Job: hhsuite_3.3.0+ds-8
Machine Architecture: armhf
Package: hhsuite
Package-Time: 2055
Source-Version: 3.3.0+ds-8
Space: 575220
Status: successful
Version: 3.3.0+ds-8
--------------------------------------------------------------------------------
Finished at 2023-09-20T05:13:00Z
Build needed 00:34:15, 575220k disc space