hhsuite →
3.3.0+ds-6 →
armhf → 2021-11-25 07:16:46
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| hhsuite 3.3.0+ds-6 (armhf) Thu, 25 Nov 2021 06:34:54 +0000 |
+==============================================================================+
Package: hhsuite
Version: 3.3.0+ds-6
Source Version: 3.3.0+ds-6
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-9c6ab9f2-29dd-4535-8513-a0c021768dd0' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.5 MB]
Fetched 26.0 MB in 27s (969 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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://172.17.0.1/private bookworm-staging/main hhsuite 3.3.0+ds-6 (dsc) [2126 B]
Get:2 http://172.17.0.1/private bookworm-staging/main hhsuite 3.3.0+ds-6 (tar) [4775 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main hhsuite 3.3.0+ds-6 (diff) [16.6 kB]
Fetched 4794 kB in 1s (6626 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hhsuite-M3hhBY/hhsuite-3.3.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hhsuite-M3hhBY' 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-RLOAbm/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-RLOAbm/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-RLOAbm/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-RLOAbm/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2788 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 35 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-RLOAbm/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 11s (77 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12500 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-RLOAbm/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-RLOAbm/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Sources [517 B]
Get:5 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ Packages [598 B]
Fetched 2448 B in 1s (2958 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file fontconfig-config fonts-dejavu-core gettext gettext-base
groff-base help2man hicolor-icon-theme imagemagick imagemagick-6-common
imagemagick-6.q16 intltool-debian libaom3 libarchive-zip-perl libarchive13
libbrotli1 libbsd0 libcurl4 libdav1d5 libde265-0 libdebhelper-perl
libdeflate0 libelf1 libexpat1 libfftw3-double3
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libheif1 libicu67 libjbig0 libjpeg62-turbo libjsoncpp24 liblcms2-2
liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6
libmagickwand-6.q16-6 libmd0 libncurses6 libncursesw6 libnghttp2-14
libopenjp2-7 libpipeline1 libpng16-16 libprocps8 libpsl5 librhash0 librtmp1
libsigsegv2 libsimde-dev libssh2-1 libsub-override-perl libtiff5 libtinfo6
libtool libuchardet0 libuv1 libwebp6 libwebpdemux2 libwebpmux3 libx11-6
libx11-data libx265-199 libxau6 libxcb1 libxdmcp6 libxext6 libxml2 m4 man-db
ncurses-bin po-debconf procps sensible-utils ucf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc 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
liblcms2-utils libmagickcore-6.q16-6-extra libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libmagickcore-6.q16-6-extra ghostscript netpbm
ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs gsfonts libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file fontconfig-config fonts-dejavu-core gettext gettext-base
groff-base help2man hicolor-icon-theme imagemagick imagemagick-6-common
imagemagick-6.q16 intltool-debian libaom3 libarchive-zip-perl libarchive13
libbrotli1 libbsd0 libcurl4 libdav1d5 libde265-0 libdebhelper-perl
libdeflate0 libelf1 libexpat1 libfftw3-double3
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0
libheif1 libicu67 libjbig0 libjpeg62-turbo libjsoncpp24 liblcms2-2
liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6
libmagickwand-6.q16-6 libmd0 libncurses6 libnghttp2-14 libopenjp2-7
libpipeline1 libpng16-16 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
libsimde-dev libssh2-1 libsub-override-perl libtiff5 libtool libuchardet0
libuv1 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libx265-199
libxau6 libxcb1 libxdmcp6 libxext6 libxml2 m4 man-db po-debconf procps
sbuild-build-depends-hhsuite-dummy sensible-utils ucf
The following packages will be upgraded:
libncursesw6 libtinfo6 ncurses-bin
3 upgraded, 90 newly installed, 0 to remove and 32 not upgraded.
Need to get 38.6 MB of archives.
After this operation, 142 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-RLOAbm/apt_archive ./ sbuild-build-depends-hhsuite-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf libtinfo6 armhf 6.3-1 [335 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf ncurses-bin armhf 6.3-1 [431 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libncursesw6 armhf 6.3-1 [105 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-3 [80.1 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf libfreetype6 armhf 2.11.0+dfsg-1 [386 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libaom3 armhf 3.2.0-1 [1233 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libdav1d5 armhf 0.9.2-1+rpi1 [199 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libde265-0 armhf 1.0.8-1+rpi1 [182 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libx265-199 armhf 3.5-2 [548 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libheif1 armhf 1.12.0-2+b3 [163 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [122 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.12~rc1-2 [121 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.1-1 [1210 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf liblqr-1-0 armhf 0.4.2-2.1 [23.1 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libopenjp2-7 armhf 2.4.0-3 [150 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libwebp6 armhf 0.6.1-2.1 [225 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libtiff5 armhf 4.3.0-2 [272 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libwebpdemux2 armhf 0.6.1-2.1 [86.8 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libwebpmux3 armhf 0.6.1-2.1 [94.4 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf imagemagick-6-common all 8:6.9.11.60+dfsg-1.3 [211 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libmagickcore-6.q16-6 armhf 8:6.9.11.60+dfsg-1.3 [1641 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libmagickwand-6.q16-6 armhf 8:6.9.11.60+dfsg-1.3 [434 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.3-1 [79.8 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libcurl4 armhf 7.79.1-2 [320 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp24 armhf 1.9.4-5 [67.4 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf librhash0 armhf 1.4.2-1 [141 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libuv1 armhf 1.42.0-1 [121 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.9 [11.2 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf cmake-data all 3.22.0-1 [1902 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf cmake armhf 3.22.0-1 [3499 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.1-1 [26.5 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.1-1 [15.6 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf help2man armhf 1.48.5 [143 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf hicolor-icon-theme all 0.17-2 [11.4 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf imagemagick-6.q16 armhf 8:6.9.11.60+dfsg-1.3 [383 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf imagemagick armhf 8:6.9.11.60+dfsg-1.3 [166 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libsimde-dev all 0.7.2-5 [259 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 38.6 MB in 6s (6926 kB/s)
(Reading database ... 12500 files and directories currently installed.)
Preparing to unpack .../libtinfo6_6.3-1_armhf.deb ...
Unpacking libtinfo6:armhf (6.3-1) over (6.2+20201114-4) ...
Setting up libtinfo6:armhf (6.3-1) ...
(Reading database ... 12500 files and directories currently installed.)
Preparing to unpack .../ncurses-bin_6.3-1_armhf.deb ...
Unpacking ncurses-bin (6.3-1) over (6.2+20201114-4) ...
Setting up ncurses-bin (6.3-1) ...
(Reading database ... 12500 files and directories currently installed.)
Preparing to unpack .../libncursesw6_6.3-1_armhf.deb ...
Unpacking libncursesw6:armhf (6.3-1) over (6.2+20201114-4) ...
Setting up libncursesw6:armhf (6.3-1) ...
Selecting previously unselected package bsdextrautils.
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update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode
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Setting up sbuild-build-depends-hhsuite-dummy (0.invalid.0) ...
Setting up imagemagick (8:6.9.11.60+dfsg-1.3) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.MdYxzMY7/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 22 21:42:42 2021 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./hhsuite_3.3.0+ds-6.dsc
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-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying test_without_mpi
dpkg-source: info: applying perlscript_uselib
dpkg-source: info: applying perl_interpreter
dpkg-source: info: applying drop-fmemopen.h.patch
dpkg-source: info: applying python3
dpkg-source: info: applying ppc64el.patch
dpkg-source: info: applying exe_suffix
Check 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
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SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-9c6ab9f2-29dd-4535-8513-a0c021768dd0
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SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package hhsuite
dpkg-buildpackage: info: source version 3.3.0+ds-6
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
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dh_auto_configure --builddirectory mybuild -- -DNATIVE_ARCH=0
cd mybuild && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DNATIVE_ARCH=0 ..
-- The C compiler identification is GNU 10.3.0
-- The CXX compiler identification is GNU 10.3.0
-- Detecting C compiler ABI info
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-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
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-- Detecting CXX compile features
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-- Compiler is GNU
-- Looking for fmemopen
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-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
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-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP
-- Configuring done
-- Generating done
CMake Warning:
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CMAKE_EXPORT_NO_PACKAGE_REGISTRY
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CMAKE_INSTALL_LIBDIR
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dh_auto_build --builddirectory mybuild
cd mybuild && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
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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/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=
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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/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color=
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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/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --color=
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[ 3%] Generating ../generated/context_data.crf.h
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && mkdir -p /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated
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.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c
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
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
[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.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 -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp
/<<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=]
291 | fprintf(stderr, "Failed to allocate %ld bytes\n", nbytes);
| ~~^ ~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
[ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o
cd /<<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.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c
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cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1
/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o
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[ 7%] Generating ../generated/context_data.lib.h
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && mkdir -p /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && /<<BUILDDIR>>/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && /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
[ 8%] Linking CXX static library libhhviterbialgorithm_with_celloff.a
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake
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
/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 8%] Built target hhviterbialgorithm_with_celloff
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
[ 9%] Generating ../generated/cs219.lib.h
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && mkdir -p /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && /<<BUILDDIR>>/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h
make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_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/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/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.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 -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 && /bin/sed 's!unsigned char!static const unsigned char!' < /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && mv -f /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h
make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.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/cs /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/cs /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
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make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.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/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
[ 12%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_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_with_celloff_and_ss.dir/link.txt --verbose=1
/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o
/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 12%] Built target hhviterbialgorithm_with_celloff_and_ss
[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.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/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs/as.cc
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && /bin/sed 's!unsigned char!static const unsigned char!' < /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/data && mv -f /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h
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[ 14%] 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
make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.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_COMPRESS.dir/DependInfo.cmake --color=
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[ 14%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.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_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
[ 15%] 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
[ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.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/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc
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/<<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
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[ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.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.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c
/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_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a
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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_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c
[ 29%] Linking C executable ffindex_from_fasta
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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/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_unpack.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 32%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.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_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c
[ 33%] Linking C executable ffindex_modify
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<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_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a
[ 34%] Linking C executable ffindex_unpack
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/<<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_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a
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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/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_order.dir/DependInfo.cmake --color=
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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_from_fasta_with_split.dir/DependInfo.cmake --color=
[ 35%] 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
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[ 36%] 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
make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_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_extract.dir/DependInfo.cmake --color=
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[ 37%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_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_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_extract.cpp
[ 38%] Linking C executable ffindex_order
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1
/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_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a
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make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.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/a3m_reduce.dir/DependInfo.cmake --color=
[ 39%] Linking C executable ffindex_from_fasta_with_split
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1
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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_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_reduce.cpp
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make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend
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make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 41%] 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
[ 42%] Linking CXX static library libCS_OBJECTS.a
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/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o
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[ 42%] Built target CS_OBJECTS
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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[ 43%] 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
[ 44%] 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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[ 44%] Built target a3m_extract
make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.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_filter.dir/DependInfo.cmake --color=
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[ 45%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.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_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp
[ 46%] 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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/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_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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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/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhblits.cpp
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/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_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.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/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
[ 52%] Linking CXX executable a3m_database_filter
cd /<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<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_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a
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[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.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/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
[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.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/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhsearch.cpp
[ 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
[ 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
In file included from /usr/include/c++/10/vector:72,
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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Hit>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
[ 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
In file included from /usr/include/c++/10/vector:67,
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++/10/bits/stl_vector.h: In member function 'void HitList::PrintMatrices(HMM*, std::stringstream&, bool, size_t, const float (*)[20])':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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
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/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp
[ 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:866,
from /usr/include/c++/10/cstdio:42,
from /usr/include/c++/10/ext/string_conversions.h:43,
from /usr/include/c++/10/bits/basic_string.h:6557,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/istream:38,
from /usr/include/c++/10/fstream:38,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.h:6,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhalignment.cpp:8:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:38:34: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.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/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhfullalignment.cpp
[ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.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/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp
[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.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/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp
[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.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/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbi.cpp
[ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.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/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp
[ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.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/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp
[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.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/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.cpp
[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.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/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp
[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.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/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp
[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.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/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
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
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++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >; _Distance = int; _Tp = std::pair<double, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: 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
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
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++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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
[ 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
[ 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++/10/vector:72,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.h:11,
from /<<BUILDDIR>>/hhsuite-3.3.0+ds/src/hhprefilter.cpp:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, int>}; _Tp = std::pair<double, int>; _Alloc = std::allocator<std::pair<double, int> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<double, int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function '_ZN9Prefilter12prefilter_dbEP3HMMP4HashI3HitEiiiiiddiiiPA20_KfRSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaISH_EESK_._omp_fn.1':
/usr/include/c++/10/bits/vector.tcc:121:21: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Hit&}; _Tp = Hit; _Alloc = std::allocator<Hit>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Hit>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
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++/10/bits/stl_vector.h: In member function 'void ViterbiConsumerThread::align(int, int, float, char)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
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++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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++/10/bits/stl_algo.h:1667:5: 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++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, int>*, std::vector<std::pair<double, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<comparePair>]':
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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++/10/bits/stl_algo.h:1964:25: 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
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: 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
1942 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function '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> > >&)':
/usr/include/c++/10/bits/stl_algo.h:1979:25: 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
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: 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
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function '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])':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function '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)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Hit*, std::vector<Hit> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 79%] Linking CXX static library libHH_OBJECTS.a
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/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.dir/hhblits_app.cpp.o -o hhalign libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a
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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:866,
from /usr/include/c++/10/cstdio:42,
from /usr/include/c++/10/ext/string_conversions.h:43,
from /usr/include/c++/10/bits/basic_string.h:6557,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/istream:38,
from /usr/include/c++/10/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:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 96%] Linking CXX executable hhblits_omp
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/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
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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:866,
from /usr/include/c++/10/cstdio:42,
from /usr/include/c++/10/ext/string_conversions.h:43,
from /usr/include/c++/10/bits/basic_string.h:6557,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/istream:38,
from /usr/include/c++/10/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:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __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:866,
from /usr/include/c++/10/cstdio:42,
from /usr/include/c++/10/ext/string_conversions.h:43,
from /usr/include/c++/10/bits/basic_string.h:6557,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/istream:38,
from /usr/include/c++/10/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:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __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
make[4]: Leaving directory '/<<BUILDDIR>>/hhsuite-3.3.0+ds/mybuild'
[ 99%] Built target hhalign_omp
/<<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:866,
from /usr/include/c++/10/cstdio:42,
from /usr/include/c++/10/ext/string_conversions.h:43,
from /usr/include/c++/10/bits/basic_string.h:6557,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/istream:38,
from /usr/include/c++/10/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:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:70:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096
70 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
71 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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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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
- 07:01:48.004 INFO: query.a3m is in A2M, A3M or FASTA format
- 07:01:54.578 INFO: Alternative alignment: 0
- 07:01:55.082 INFO: 1 alignments done
- 07:01:55.441 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 Thu Nov 25 07:01:56 2021
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 5147 0
query.a3m 0 32666 26 0
query.a3m 0 32666 1019 0
Reading context library for pseudocounts from internal ...
Reading abstract state alphabet from internal ...
Processing entry: query.a3m
Adding cs-pseudocounts (admix=0.30) ...
- 07:02:17.124 INFO: Searching 1 column state sequences.
- 07:02:17.808 INFO: query.a3m is in A2M, A3M or FASTA format
- 07:02:18.067 INFO: Iteration 1
- 07:02:23.677 INFO: Prefiltering database
- 07:02:29.353 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 07:02:29.380 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 07:02:29.381 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 07:02:29.381 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 07:02:29.902 INFO: Alternative alignment: 0
- 07:02:30.390 INFO: 1 alignments done
- 07:02:30.391 INFO: Alternative alignment: 1
- 07:02:30.881 INFO: 1 alignments done
- 07:02:30.882 INFO: Alternative alignment: 2
- 07:02:30.883 INFO: Alternative alignment: 3
- 07:02:37.399 INFO: Premerge done
- 07:02:37.400 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 07:02:37.900 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 Thu Nov 25 07:02:37 2021
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)
- 07:02:38.126 INFO: Searching 1 column state sequences.
- 07:02:38.663 INFO: Thread 1 query.a3m
- 07:02:38.799 INFO: query.a3m is in A2M, A3M or FASTA format
- 07:02:39.064 INFO: Iteration 1
- 07:02:50.164 INFO: Prefiltering database
- 07:03:01.336 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1
- 07:03:01.363 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1
- 07:03:01.364 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1
- 07:03:01.365 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 07:03:01.636 INFO: Alternative alignment: 0
- 07:03:02.123 INFO: 1 alignments done
- 07:03:02.124 INFO: Alternative alignment: 1
- 07:03:02.612 INFO: 1 alignments done
- 07:03:02.613 INFO: Alternative alignment: 2
- 07:03:02.613 INFO: Alternative alignment: 3
- 07:03:14.405 INFO: Premerge done
- 07:03:14.406 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 07:03:14.809 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001
- 07:03:16.102 INFO: query.a3m is in A2M, A3M or FASTA format
- 07:03:16.361 INFO: Searching 1 database HHMs without prefiltering
- 07:03:16.361 INFO: Iteration 1
- 07:03:21.964 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 07:03:22.483 INFO: Alternative alignment: 0
- 07:03:22.971 INFO: 1 alignments done
- 07:03:22.971 INFO: Alternative alignment: 1
- 07:03:23.459 INFO: 1 alignments done
- 07:03:23.459 INFO: Alternative alignment: 2
- 07:03:23.460 INFO: Alternative alignment: 3
- 07:03:29.988 INFO: Premerge done
- 07:03:29.989 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 07:03:30.490 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 Thu Nov 25 07:03:30 2021
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)
- 07:03:31.245 INFO: Thread 0 query.a3m
- 07:03:31.377 INFO: query.a3m is in A2M, A3M or FASTA format
- 07:03:31.636 INFO: Searching 1 database HHMs without prefiltering
- 07:03:31.636 INFO: Iteration 1
- 07:03:42.716 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment
- 07:03:42.979 INFO: Alternative alignment: 0
- 07:03:43.463 INFO: 1 alignments done
- 07:03:43.464 INFO: Alternative alignment: 1
- 07:03:43.952 INFO: 1 alignments done
- 07:03:43.952 INFO: Alternative alignment: 2
- 07:03:43.953 INFO: Alternative alignment: 3
- 07:03:55.714 INFO: Premerge done
- 07:03:55.715 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm
- 07:03:56.114 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'
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-- 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/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/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_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/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/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/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/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/hhsearch_omp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hhsuite/usr/bin/a3m_database_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/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_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/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/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/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: package could avoid a useless dependency if debian/hhsuite/usr/bin/ffindex_build debian/hhsuite/usr/bin/hhmake debian/hhsuite/usr/bin/ffindex_apply debian/hhsuite/usr/bin/a3m_extract debian/hhsuite/usr/bin/a3m_database_extract debian/hhsuite/usr/bin/hhblits_omp debian/hhsuite/usr/bin/ffindex_reduce debian/hhsuite/usr/bin/hhsearch debian/hhsuite/usr/bin/hhfilter debian/hhsuite/usr/bin/hhalign_omp debian/hhsuite/usr/bin/hhblits_ca3m debian/hhsuite/usr/bin/ffindex_from_fasta_with_split debian/hhsuite/usr/bin/hhsearch_omp debian/hhsuite/usr/bin/a3m_database_filter debian/hhsuite/usr/bin/hhblits debian/hhsuite/usr/bin/ffindex_from_fasta debian/hhsuite/usr/bin/a3m_database_reduce debian/hhsuite/usr/bin/a3m_reduce debian/hhsuite/usr/bin/hhalign debian/hhsuite/usr/bin/hhconsensus debian/hhsuite/usr/bin/ffindex_modify debian/hhsuite/usr/bin/ffindex_get debian/hhsuite/usr/libexec/hhsuite/bin/cstranslate debian/hhsuite/usr/bin/ffindex_unpack debian/hhsuite/usr/bin/ffindex_order 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 (= 0.7.2-5), "
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-6_armhf.deb'.
dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-6_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../hhsuite_3.3.0+ds-6_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 2021-11-25T07:16:19Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
hhsuite_3.3.0+ds-6_armhf.changes:
---------------------------------
Format: 1.8
Date: Mon, 22 Nov 2021 22:27:31 +0100
Source: hhsuite
Binary: hhsuite hhsuite-dbgsym
Architecture: armhf
Version: 3.3.0+ds-6
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
Changes:
hhsuite (3.3.0+ds-6) unstable; urgency=medium
.
* Adjust patch to not overwrite example files in tests.
This caused a modified file containing the build time to be packaged,
leaving the package unreproducible (and is likely not intended here)
Checksums-Sha1:
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f6ba4d2d89d29adcb36be411aa25b4c9602c0f42 6895 hhsuite_3.3.0+ds-6_armhf.buildinfo
614ea2cb8c28f92dd97e9290dcfb70c12f102f1d 10228924 hhsuite_3.3.0+ds-6_armhf.deb
Checksums-Sha256:
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75c3c5bb28e10417310281419fe2225e37ab5ef51ce7728394287c583a769740 6895 hhsuite_3.3.0+ds-6_armhf.buildinfo
896d03a1eca778c3b67773a87b715ab8f9b746a828a77493db1b642c554ea8a4 10228924 hhsuite_3.3.0+ds-6_armhf.deb
Files:
48bce358d2934a280edf023c598dae18 17447676 debug optional hhsuite-dbgsym_3.3.0+ds-6_armhf.deb
d1973278731fd9151d079778ce0fa9d1 6895 science optional hhsuite_3.3.0+ds-6_armhf.buildinfo
b1fe697a5a5968de1707e977bb6f6820 10228924 science optional hhsuite_3.3.0+ds-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
hhsuite-dbgsym_3.3.0+ds-6_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 17447676 bytes: control archive=1740 bytes.
1362 bytes, 12 lines control
2737 bytes, 26 lines md5sums
Package: hhsuite-dbgsym
Source: hhsuite
Version: 3.3.0+ds-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18223
Depends: hhsuite (= 3.3.0+ds-6)
Section: debug
Priority: optional
Description: debug symbols for hhsuite
Build-Ids: 0e1ee22131e70249542eeab851840369ddfc85ed 0f3f3a7b6dca373d675f124f0a09c43febb3dcb2 10bd074d4f3796d20dfb835a30de49c4319e65bd 14d0548f170aa6fa5c2ac3ba5f32659126a14917 223fc170853b17ddb2a0f23b8f44d8757ef4c76b 22611bf66cf2feca442721b3937f0bb62dd86243 2b0453a58c16d243e4386c54fdfbc8d3d5364752 2fde9d3a592238d45c9a4721251a2afed0c4733e 37179981cc30a6d797adf5e8b8b2c6279e7e7a5f 3726bc487791caf3343fb8f432a406bce0b2d79a 452a9deecb5e824841fcdc43688db49073886fbd 525b6ee347a5503cf4a56cd131f5bab18244a75e 90eedb603ed505ea22afda693cfafdc193d893ec 94995332069fe962d2f82b46f31b3bc25913647c 9fcf3be7b14d54c3e80a962be77fbc6fe8a695a8 a39e8d07fcff0d556bf50331996363760470361f a724e2b7e9ec815247e2cc2a82e5bc21d0da4812 a73d53b2c066c8fe8c4811ae4744b7220d86f570 a931ca655cdaf7cdbb5377caa640a2f87204b524 b1e5b12ae785548fdbea922bb60a8f6a77429369 bf983f9cab71c35f3d969a9e9f361c330f7df004 dc22b2d96493583c41c6ea7a73652172f61c040e e15087d4c6857f51683be2a56270ad06a5704ac0 e39d3b204860b531055743c5c8e4fd41eaf874d2 f5b3392663f4fb5bc90125b33a7d1b5c0a72fded
drwxr-xr-x root/root 0 2021-11-22 21:27 ./
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/0e/
-rw-r--r-- root/root 22324 2021-11-22 21:27 ./usr/lib/debug/.build-id/0e/1ee22131e70249542eeab851840369ddfc85ed.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/0f/
-rw-r--r-- root/root 105996 2021-11-22 21:27 ./usr/lib/debug/.build-id/0f/3f3a7b6dca373d675f124f0a09c43febb3dcb2.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/10/
-rw-r--r-- root/root 2110240 2021-11-22 21:27 ./usr/lib/debug/.build-id/10/bd074d4f3796d20dfb835a30de49c4319e65bd.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/14/
-rw-r--r-- root/root 23852 2021-11-22 21:27 ./usr/lib/debug/.build-id/14/d0548f170aa6fa5c2ac3ba5f32659126a14917.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/22/
-rw-r--r-- root/root 23368 2021-11-22 21:27 ./usr/lib/debug/.build-id/22/3fc170853b17ddb2a0f23b8f44d8757ef4c76b.debug
-rw-r--r-- root/root 721408 2021-11-22 21:27 ./usr/lib/debug/.build-id/22/611bf66cf2feca442721b3937f0bb62dd86243.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/2b/
-rw-r--r-- root/root 25152 2021-11-22 21:27 ./usr/lib/debug/.build-id/2b/0453a58c16d243e4386c54fdfbc8d3d5364752.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/2f/
-rw-r--r-- root/root 2139872 2021-11-22 21:27 ./usr/lib/debug/.build-id/2f/de9d3a592238d45c9a4721251a2afed0c4733e.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/37/
-rw-r--r-- root/root 25332 2021-11-22 21:27 ./usr/lib/debug/.build-id/37/179981cc30a6d797adf5e8b8b2c6279e7e7a5f.debug
-rw-r--r-- root/root 2070172 2021-11-22 21:27 ./usr/lib/debug/.build-id/37/26bc487791caf3343fb8f432a406bce0b2d79a.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/45/
-rw-r--r-- root/root 28204 2021-11-22 21:27 ./usr/lib/debug/.build-id/45/2a9deecb5e824841fcdc43688db49073886fbd.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/52/
-rw-r--r-- root/root 99488 2021-11-22 21:27 ./usr/lib/debug/.build-id/52/5b6ee347a5503cf4a56cd131f5bab18244a75e.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/90/
-rw-r--r-- root/root 23084 2021-11-22 21:27 ./usr/lib/debug/.build-id/90/eedb603ed505ea22afda693cfafdc193d893ec.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/94/
-rw-r--r-- root/root 23108 2021-11-22 21:27 ./usr/lib/debug/.build-id/94/995332069fe962d2f82b46f31b3bc25913647c.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/9f/
-rw-r--r-- root/root 104056 2021-11-22 21:27 ./usr/lib/debug/.build-id/9f/cf3be7b14d54c3e80a962be77fbc6fe8a695a8.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/a3/
-rw-r--r-- root/root 136896 2021-11-22 21:27 ./usr/lib/debug/.build-id/a3/9e8d07fcff0d556bf50331996363760470361f.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/a7/
-rw-r--r-- root/root 23040 2021-11-22 21:27 ./usr/lib/debug/.build-id/a7/24e2b7e9ec815247e2cc2a82e5bc21d0da4812.debug
-rw-r--r-- root/root 2014972 2021-11-22 21:27 ./usr/lib/debug/.build-id/a7/3d53b2c066c8fe8c4811ae4744b7220d86f570.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/a9/
-rw-r--r-- root/root 566084 2021-11-22 21:27 ./usr/lib/debug/.build-id/a9/31ca655cdaf7cdbb5377caa640a2f87204b524.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/b1/
-rw-r--r-- root/root 2016880 2021-11-22 21:27 ./usr/lib/debug/.build-id/b1/e5b12ae785548fdbea922bb60a8f6a77429369.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 106520 2021-11-22 21:27 ./usr/lib/debug/.build-id/bf/983f9cab71c35f3d969a9e9f361c330f7df004.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/dc/
-rw-r--r-- root/root 1975084 2021-11-22 21:27 ./usr/lib/debug/.build-id/dc/22b2d96493583c41c6ea7a73652172f61c040e.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 2100160 2021-11-22 21:27 ./usr/lib/debug/.build-id/e1/5087d4c6857f51683be2a56270ad06a5704ac0.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/e3/
-rw-r--r-- root/root 864412 2021-11-22 21:27 ./usr/lib/debug/.build-id/e3/9d3b204860b531055743c5c8e4fd41eaf874d2.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.build-id/f5/
-rw-r--r-- root/root 771480 2021-11-22 21:27 ./usr/lib/debug/.build-id/f5/b3392663f4fb5bc90125b33a7d1b5c0a72fded.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 493576 2021-11-22 21:27 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/hhsuite.debug
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/share/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-11-22 21:27 ./usr/share/doc/hhsuite-dbgsym -> hhsuite
hhsuite_3.3.0+ds-6_armhf.deb
----------------------------
new Debian package, version 2.0.
size 10228924 bytes: control archive=2816 bytes.
1470 bytes, 29 lines control
4311 bytes, 65 lines md5sums
Package: hhsuite
Version: 3.3.0+ds-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 76503
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 9), perl:any, hhsuite-data (= 3.3.0+ds-6), python3
Conflicts: ffindex
Built-Using: simde (= 0.7.2-5)
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 2021-11-22 21:27 ./
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/bin/
-rwxr-xr-x root/root 38548 2021-11-22 21:27 ./usr/bin/a3m_database_extract
-rwxr-xr-x root/root 42644 2021-11-22 21:27 ./usr/bin/a3m_database_filter
-rwxr-xr-x root/root 38548 2021-11-22 21:27 ./usr/bin/a3m_database_reduce
-rwxr-xr-x root/root 38548 2021-11-22 21:27 ./usr/bin/a3m_extract
-rwxr-xr-x root/root 38548 2021-11-22 21:27 ./usr/bin/a3m_reduce
-rwxr-xr-x root/root 22192 2021-11-22 21:27 ./usr/bin/ffindex_apply
-rwxr-xr-x root/root 18128 2021-11-22 21:27 ./usr/bin/ffindex_build
-rwxr-xr-x root/root 18064 2021-11-22 21:27 ./usr/bin/ffindex_from_fasta
-rwxr-xr-x root/root 18016 2021-11-22 21:27 ./usr/bin/ffindex_from_fasta_with_split
-rwxr-xr-x root/root 18048 2021-11-22 21:27 ./usr/bin/ffindex_get
-rwxr-xr-x root/root 18096 2021-11-22 21:27 ./usr/bin/ffindex_modify
-rwxr-xr-x root/root 18016 2021-11-22 21:27 ./usr/bin/ffindex_order
-rwxr-xr-x root/root 18016 2021-11-22 21:27 ./usr/bin/ffindex_reduce
-rwxr-xr-x root/root 18016 2021-11-22 21:27 ./usr/bin/ffindex_unpack
-rwxr-xr-x root/root 7972512 2021-11-22 21:27 ./usr/bin/hhalign
-rwxr-xr-x root/root 7984800 2021-11-22 21:27 ./usr/bin/hhalign_omp
-rwxr-xr-x root/root 7935648 2021-11-22 21:27 ./usr/bin/hhblits
-rwxr-xr-x root/root 7943840 2021-11-22 21:27 ./usr/bin/hhblits_ca3m
-rwxr-xr-x root/root 7947936 2021-11-22 21:27 ./usr/bin/hhblits_omp
-rwxr-xr-x root/root 7517852 2021-11-22 21:27 ./usr/bin/hhconsensus
-rwxr-xr-x root/root 263832 2021-11-22 21:27 ./usr/bin/hhfilter
-rwxr-xr-x root/root 7501468 2021-11-22 21:27 ./usr/bin/hhmake
-rwxr-xr-x root/root 7964320 2021-11-22 21:27 ./usr/bin/hhsearch
-rwxr-xr-x root/root 7976608 2021-11-22 21:27 ./usr/bin/hhsearch_omp
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/
lrwxrwxrwx root/root 0 2021-11-22 21:27 ./usr/lib/hh -> hhsuite
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/lib/hhsuite/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./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 2021-11-22 21:27 ./usr/lib/hhsuite/scripts -> ../../share/hhsuite/scripts
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/libexec/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/libexec/hhsuite/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/libexec/hhsuite/bin/
-rwxr-xr-x root/root 6190760 2021-11-22 21:27 ./usr/libexec/hhsuite/bin/cstranslate
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/share/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./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 3241 2021-11-22 21:27 ./usr/share/doc/hhsuite/changelog.Debian.gz
-rw-r--r-- root/root 20347 2021-11-22 21:27 ./usr/share/doc/hhsuite/copyright
drwxr-xr-x root/root 0 2021-11-22 21:27 ./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 2021-11-22 21:27 ./usr/share/hhsuite/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./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 2021-11-22 21:27 ./usr/share/hhsuite/scripts/a3m.py
-rwxr-xr-x root/root 31681 2021-11-22 21:27 ./usr/share/hhsuite/scripts/addss.pl
-rwxr-xr-x root/root 438 2021-11-22 21:27 ./usr/share/hhsuite/scripts/check_a3m.py
-rwxr-xr-x root/root 28735 2021-11-22 21:27 ./usr/share/hhsuite/scripts/cif2fasta.py
-rwxr-xr-x root/root 4654 2021-11-22 21:27 ./usr/share/hhsuite/scripts/create_profile_from_hhm.pl
-rwxr-xr-x root/root 6815 2021-11-22 21:27 ./usr/share/hhsuite/scripts/create_profile_from_hmmer.pl
-rwxr-xr-x root/root 2081 2021-11-22 21:27 ./usr/share/hhsuite/scripts/ffindex.py
-rwxr-xr-x root/root 446 2021-11-22 21:27 ./usr/share/hhsuite/scripts/get_a3m_size.py
-rwxr-xr-x root/root 7179 2021-11-22 21:27 ./usr/share/hhsuite/scripts/hh_reader.py
-rwxr-xr-x root/root 48079 2021-11-22 21:27 ./usr/share/hhsuite/scripts/hhmakemodel.pl
-rwxr-xr-x root/root 87343 2021-11-22 21:27 ./usr/share/hhsuite/scripts/hhmakemodel.py
-rwxr-xr-x root/root 16961 2021-11-22 21:27 ./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 2021-11-22 21:27 ./usr/share/hhsuite/scripts/multithread.pl
-rwxr-xr-x root/root 40490 2021-11-22 21:27 ./usr/share/hhsuite/scripts/pdb2fasta.pl
-rwxr-xr-x root/root 13183 2021-11-22 21:27 ./usr/share/hhsuite/scripts/pdbfilter.pl
-rwxr-xr-x root/root 8648 2021-11-22 21:27 ./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 2021-11-22 21:27 ./usr/share/hhsuite/scripts/renumberpdb.pl
-rwxr-xr-x root/root 3651 2021-11-22 21:27 ./usr/share/hhsuite/scripts/splitfasta.pl
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/share/man/
drwxr-xr-x root/root 0 2021-11-22 21:27 ./usr/share/man/man1/
-rw-r--r-- root/root 3090 2021-11-22 21:27 ./usr/share/man/man1/hhalign.1.gz
-rw-r--r-- root/root 4142 2021-11-22 21:27 ./usr/share/man/man1/hhblits.1.gz
-rw-r--r-- root/root 4152 2021-11-22 21:27 ./usr/share/man/man1/hhblits_omp.1.gz
-rw-r--r-- root/root 1029 2021-11-22 21:27 ./usr/share/man/man1/hhconsensus.1.gz
-rw-r--r-- root/root 1021 2021-11-22 21:27 ./usr/share/man/man1/hhfilter.1.gz
-rw-r--r-- root/root 1656 2021-11-22 21:27 ./usr/share/man/man1/hhmake.1.gz
-rw-r--r-- root/root 3358 2021-11-22 21:27 ./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: 600184
Build-Time: 1567
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 831
Job: hhsuite_3.3.0+ds-6
Machine Architecture: armhf
Package: hhsuite
Package-Time: 2485
Source-Version: 3.3.0+ds-6
Space: 600184
Status: successful
Version: 3.3.0+ds-6
--------------------------------------------------------------------------------
Finished at 2021-11-25T07:16:19Z
Build needed 00:41:25, 600184k disc space