Tue 18 Sep 21:55:55 BST 2018: starting build of hmmer version 3.2.1+dfsg-1 arch armel on mustang5 Running apt-get -q --download-only --only-source source hmmer=3.2.1+dfsg-1 Reading package lists... NOTICE: 'hmmer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hmmer.git Please use: git clone https://salsa.debian.org/med-team/hmmer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5,985 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main hmmer 3.2.1+dfsg-1 (dsc) [2,101 B] Get:2 http://mirror.einval.org/debian unstable/main hmmer 3.2.1+dfsg-1 (tar) [5,974 kB] Get:3 http://mirror.einval.org/debian unstable/main hmmer 3.2.1+dfsg-1 (diff) [9,040 B] Fetched 5,985 kB in 0s (39.3 MB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'hmmer_3.2.1+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) total 5852 -rw-r--r-- 1 root root 9040 Aug 24 08:37 hmmer_3.2.1+dfsg-1.debian.tar.xz -rw-r--r-- 1 root root 2101 Aug 24 08:37 hmmer_3.2.1+dfsg-1.dsc -rw-r--r-- 1 root root 5974072 Aug 24 08:37 hmmer_3.2.1+dfsg.orig.tar.xz W: /root/.pbuilderrc does not exist I: using fakeroot in build. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 18 21:55:56 BST 2018 I: pbuilder-time-stamp: 1537304156 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-armel.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: Mounting /dev I: Mounting /dev/pts I: Mounting /proc I: Mounting /sys I: policy-rc.d already exists I: Obtaining the cached apt archive contents I: Copying source file I: copying [hmmer_3.2.1+dfsg-1.dsc] I: copying [./hmmer_3.2.1+dfsg.orig.tar.xz] I: copying [./hmmer_3.2.1+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Aug 24 07:25:36 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hmmer_3.2.1+dfsg-1.dsc dpkg-source: info: extracting hmmer in hmmer-3.2.1+dfsg dpkg-source: info: unpacking hmmer_3.2.1+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer_3.2.1+dfsg-1.debian.tar.xz dpkg-source: info: applying fix_manpage_extension.patch dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch I: Installing the build-deps I: user script /chroot/rebuildd/pbuilder/11096/tmp/hooks/D01update starting Get:1 http://mirror.einval.org/debian sid InRelease [233 kB] Ign:2 http://mirror.einval.org/debian sid/main armel Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main armel Packages.diff/Index [27.9 kB] Ign:2 http://mirror.einval.org/debian sid/main armel Packages.diff/Index Get:3 http://mirror.einval.org/debian sid/main armel Packages [7934 kB] Fetched 8167 kB in 4s (2180 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libncurses6 libprocps7 lsb-base Recommended packages: libgpm2 psmisc The following NEW packages will be installed: libncurses6 libprocps7 lsb-base procps debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 4 newly installed, 0 to remove and 49 not upgraded. Need to get 0 B/415 kB of archives. After this operation, 1113 kB of additional disk space will be used. Selecting previously unselected package libncurses6:armel. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11698 files and directories currently installed.) Preparing to unpack .../libncurses6_6.1+20180714-1_armel.deb ... Unpacking libncurses6:armel (6.1+20180714-1) ... Selecting previously unselected package libprocps7:armel. Preparing to unpack .../libprocps7_2%3a3.3.15-2_armel.deb ... Unpacking libprocps7:armel (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../lsb-base_9.20170808_all.deb ... Unpacking lsb-base (9.20170808) ... Selecting previously unselected package procps. Preparing to unpack .../procps_2%3a3.3.15-2_armel.deb ... Unpacking procps (2:3.3.15-2) ... Setting up libprocps7:armel (2:3.3.15-2) ... Setting up lsb-base (9.20170808) ... Processing triggers for libc-bin (2.27-5) ... Setting up libncurses6:armel (6.1+20180714-1) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Processing triggers for libc-bin (2.27-5) ... I: user script /chroot/rebuildd/pbuilder/11096/tmp/hooks/D01update finished W: skipping an editor backup file /chroot/rebuildd/pbuilder/11096/tmp/hooks/D01update~ I: user script /chroot/rebuildd/pbuilder/11096/tmp/hooks/D02enable_swp starting I: user script /chroot/rebuildd/pbuilder/11096/tmp/hooks/D02enable_swp finished W: skipping an editor backup file /chroot/rebuildd/pbuilder/11096/tmp/hooks/D02enable_swp~ -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armel Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), libdivsufsort-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 11783 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu-le-hb0{a} libicu60{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpng16-16{a} libsigsegv2{a} libtimedate-perl{a} libtool{a} libxml2{a} m4{a} man-db{a} po-debconf{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 38 newly installed, 0 to remove and 49 not upgraded. Need to get 70.8 kB/19.7 MB of archives. After unpacking 68.2 MB will be used. Writing extended state information... Get: 1 http://mirror.einval.org/debian sid/main armel libdivsufsort3 armel 2.0.1-3 [43.5 kB] Get: 2 http://mirror.einval.org/debian sid/main armel libdivsufsort-dev armel 2.0.1-3 [27.3 kB] Fetched 70.8 kB in 0s (2160 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armel. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11783 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-1_armel.deb ... Unpacking libbsd0:armel (0.9.1-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armel.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.3-10_armel.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:armel. Preparing to unpack .../03-libpipeline1_1.5.0-1_armel.deb ... Unpacking libpipeline1:armel (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.8.4-2_armel.deb ... Unpacking man-db (2.8.4-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.34-2_armel.deb ... Unpacking libmagic-mgc (1:5.34-2) ... Selecting previously unselected package libmagic1:armel. Preparing to unpack .../06-libmagic1_1%3a5.34-2_armel.deb ... Unpacking libmagic1:armel (1:5.34-2) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.34-2_armel.deb ... Unpacking file (1:5.34-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-gettext-base_0.19.8.1-7_armel.deb ... Unpacking gettext-base (0.19.8.1-7) ... Selecting previously unselected package libsigsegv2:armel. Preparing to unpack .../09-libsigsegv2_2.12-2_armel.deb ... Unpacking libsigsegv2:armel (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.18-1_armel.deb ... Unpacking m4 (1.4.18-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.1-1.1_all.deb ... Unpacking automake (1:1.16.1-1.1) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.19.8.1-7_all.deb ... Unpacking autopoint (0.19.8.1-7) ... Selecting previously unselected package libtool. Preparing to unpack .../15-libtool_2.4.6-4_all.deb ... Unpacking libtool (2.4.6-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../16-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../17-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../18-libfile-stripnondeterminism-perl_0.042-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.042-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../19-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_0.042-1_all.deb ... Unpacking dh-strip-nondeterminism (0.042-1) ... Selecting previously unselected package libelf1:armel. Preparing to unpack .../21-libelf1_0.170-0.5_armel.deb ... Unpacking libelf1:armel (0.170-0.5) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.12-2_armel.deb ... Unpacking dwz (0.12-2) ... Selecting previously unselected package libglib2.0-0:armel. Preparing to unpack .../23-libglib2.0-0_2.58.0-3_armel.deb ... Unpacking libglib2.0-0:armel (2.58.0-3) ... Selecting previously unselected package libpng16-16:armel. Preparing to unpack .../24-libpng16-16_1.6.34-2_armel.deb ... Unpacking libpng16-16:armel (1.6.34-2) ... Selecting previously unselected package libfreetype6:armel. Preparing to unpack .../25-libfreetype6_2.8.1-2_armel.deb ... Unpacking libfreetype6:armel (2.8.1-2) ... Selecting previously unselected package libgraphite2-3:armel. Preparing to unpack .../26-libgraphite2-3_1.3.12-1_armel.deb ... Unpacking libgraphite2-3:armel (1.3.12-1) ... Selecting previously unselected package libharfbuzz0b:armel. Preparing to unpack .../27-libharfbuzz0b_1.8.8-2_armel.deb ... Unpacking libharfbuzz0b:armel (1.8.8-2) ... Selecting previously unselected package libicu-le-hb0:armel. Preparing to unpack .../28-libicu-le-hb0_1.0.3+git161113-5_armel.deb ... Unpacking libicu-le-hb0:armel (1.0.3+git161113-5) ... Selecting previously unselected package libicu60:armel. Preparing to unpack .../29-libicu60_60.2-6_armel.deb ... Unpacking libicu60:armel (60.2-6) ... Selecting previously unselected package libxml2:armel. Preparing to unpack .../30-libxml2_2.9.4+dfsg1-7+b1_armel.deb ... Unpacking libxml2:armel (2.9.4+dfsg1-7+b1) ... Selecting previously unselected package libcroco3:armel. Preparing to unpack .../31-libcroco3_0.6.12-2_armel.deb ... Unpacking libcroco3:armel (0.6.12-2) ... Selecting previously unselected package gettext. Preparing to unpack .../32-gettext_0.19.8.1-7_armel.deb ... Unpacking gettext (0.19.8.1-7) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../33-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../34-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../35-debhelper_11.4_all.deb ... Unpacking debhelper (11.4) ... Selecting previously unselected package libdivsufsort3:armel. Preparing to unpack .../36-libdivsufsort3_2.0.1-3_armel.deb ... Unpacking libdivsufsort3:armel (2.0.1-3) ... Selecting previously unselected package libdivsufsort-dev:armel. Preparing to unpack .../37-libdivsufsort-dev_2.0.1-3_armel.deb ... Unpacking libdivsufsort-dev:armel (2.0.1-3) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libdivsufsort3:armel (2.0.1-3) ... Setting up libpng16-16:armel (1.6.34-2) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:armel (2.12-2) ... Setting up libelf1:armel (0.170-0.5) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:armel (2.58.0-3) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-7) ... Setting up libpipeline1:armel (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:armel (0.9.1-1) ... Setting up libfreetype6:armel (2.8.1-2) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:armel (1:5.34-2) ... Setting up libgraphite2-3:armel (1.3.12-1) ... Processing triggers for libc-bin (2.27-5) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-7) ... Setting up libfile-stripnondeterminism-perl (0.042-1) ... Setting up libdivsufsort-dev:armel (2.0.1-3) ... Setting up libharfbuzz0b:armel (1.8.8-2) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up automake (1:1.16.1-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.4-2) ... Building database of manual pages ... Setting up libtool (2.4.6-4) ... Setting up libicu-le-hb0:armel (1.0.3+git161113-5) ... Setting up libicu60:armel (60.2-6) ... Setting up libxml2:armel (2.9.4+dfsg1-7+b1) ... Setting up libcroco3:armel (0.6.12-2) ... Setting up gettext (0.19.8.1-7) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.20) ... Setting up debhelper (11.4) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (0.042-1) ... Processing triggers for libc-bin (2.27-5) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfakeroot The following NEW packages will be installed: fakeroot libfakeroot debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 2 newly installed, 0 to remove and 49 not upgraded. Need to get 0 B/129 kB of archives. After this operation, 348 kB of additional disk space will be used. Selecting previously unselected package libfakeroot:armel. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13893 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.23-1_armel.deb ... Unpacking libfakeroot:armel (1.23-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.23-1_armel.deb ... Unpacking fakeroot (1.23-1) ... Processing triggers for libc-bin (2.27-5) ... Setting up libfakeroot:armel (1.23-1) ... Processing triggers for man-db (2.8.4-2) ... Setting up fakeroot (1.23-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.27-5) ... I: Copying back the cached apt archive contents I: new cache content 'libdivsufsort3_2.0.1-3_armel.deb' added I: new cache content 'libdivsufsort-dev_2.0.1-3_armel.deb' added I: Building the package I: Running cd /build/hmmer-3.2.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us -uc -rfakeroot dpkg-buildpackage: info: source package hmmer dpkg-buildpackage: info: source version 3.2.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build hmmer-3.2.1+dfsg dpkg-buildpackage: info: host architecture armel fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/hmmer-3.2.1+dfsg' dh_auto_clean rm -f testsuite/esltmp* rm -f easel/testsuite/esltmp* rm -f tutorial/MADE1.hmm.h3? make[1]: Leaving directory '/build/hmmer-3.2.1+dfsg' dh_clean dpkg-source -b hmmer-3.2.1+dfsg dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building hmmer using existing ./hmmer_3.2.1+dfsg.orig.tar.xz dpkg-source: info: building hmmer in hmmer_3.2.1+dfsg-1.debian.tar.xz dpkg-source: info: building hmmer in hmmer_3.2.1+dfsg-1.dsc debian/rules build dh build dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/hmmer-3.2.1+dfsg' AUTOHEADER=true dh_autoreconf make[1]: Leaving directory '/build/hmmer-3.2.1+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/hmmer-3.2.1+dfsg' dh_auto_configure -- --enable-threads ./configure --build=arm-linux-gnueabi --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --libexecdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking configure: Configuring HMMER3 for your system. checking build system type... arm-unknown-linux-gnueabi checking host system type... arm-unknown-linux-gnueabi checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether ln -s works... yes checking for C compiler vendor... gnu checking for gcc option to accept ISO C99... none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether gcc can compile our Altivec/VMX code... no checking whether gcc can compile our SSE code... no configure: ::::::::::--- no vector instruction set ---:::::::::: configure: HMMER3 requires SSE or VMX vector instructions. configure: Supported platforms are x86 (Intel/AMD) and PowerPC. configure: error: No supported vectorization found for your machine. tail -v -n \+0 config.log ==> config.log <== This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by HMMER configure 3.2.1, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure --build=arm-linux-gnueabi --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=${prefix}/lib/arm-linux-gnueabi --libexecdir=${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads ## --------- ## ## Platform. ## ## --------- ## hostname = mustang5 uname -m = aarch64 uname -r = 4.9.0-8-arm64 uname -s = Linux uname -v = #1 SMP Debian 4.9.110-3+deb9u4 (2018-08-21) /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/sbin PATH: /usr/bin PATH: /sbin PATH: /bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2286: Configuring HMMER3 for your system. configure:2435: checking build system type configure:2449: result: arm-unknown-linux-gnueabi configure:2469: checking host system type configure:2482: result: arm-unknown-linux-gnueabi configure:2665: checking for gcc configure:2681: found /usr/bin/gcc configure:2692: result: gcc configure:2921: checking for C compiler version configure:2930: gcc --version >&5 gcc (Debian 8.2.0-4) 8.2.0 Copyright (C) 2018 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2941: $? = 0 configure:2930: gcc -v >&5 Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabi/8/lto-wrapper Target: arm-linux-gnueabi Configured with: ../src/configure -v --with-pkgversion='Debian 8.2.0-4' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=arm-linux-gnueabi- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv5te --with-float=soft --disable-werror --enable-checking=release --build=arm-linux-gnueabi --host=arm-linux-gnueabi --target=arm-linux-gnueabi Thread model: posix gcc version 8.2.0 (Debian 8.2.0-4) configure:2941: $? = 0 configure:2930: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:2941: $? = 1 configure:2930: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion'; did you mean '--version'? gcc: fatal error: no input files compilation terminated. configure:2941: $? = 1 configure:2961: checking whether the C compiler works configure:2983: gcc -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 configure:2987: $? = 0 configure:3035: result: yes configure:3038: checking for C compiler default output file name configure:3040: result: a.out configure:3046: checking for suffix of executables configure:3053: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 configure:3057: $? = 0 configure:3079: result: configure:3101: checking whether we are cross compiling configure:3109: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 configure:3113: $? = 0 configure:3120: ./conftest configure:3124: $? = 0 configure:3139: result: no configure:3144: checking for suffix of object files configure:3166: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3170: $? = 0 configure:3191: result: o configure:3195: checking whether we are using the GNU C compiler configure:3214: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3214: $? = 0 configure:3223: result: yes configure:3232: checking whether gcc accepts -g configure:3252: gcc -c -g -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3252: $? = 0 configure:3293: result: yes configure:3310: checking for gcc option to accept ISO C89 configure:3373: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3373: $? = 0 configure:3386: result: none needed configure:3411: checking how to run the C preprocessor configure:3442: gcc -E -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c configure:3442: $? = 0 configure:3456: gcc -E -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c conftest.c:19:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:3456: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | #include configure:3481: result: gcc -E configure:3501: gcc -E -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c configure:3501: $? = 0 configure:3515: gcc -E -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c conftest.c:19:10: fatal error: ac_nonexistent.h: No such file or directory #include ^~~~~~~~~~~~~~~~~~ compilation terminated. configure:3515: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | #include configure:3557: checking for a BSD-compatible install configure:3625: result: /usr/bin/install -c configure:3679: checking for ranlib configure:3695: found /usr/bin/ranlib configure:3706: result: ranlib configure:3730: checking for ar configure:3749: found /usr/bin/ar configure:3762: result: /usr/bin/ar configure:3770: checking whether ln -s works configure:3774: result: yes configure:3784: checking for C compiler vendor configure:3831: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 conftest.c: In function 'main': conftest.c:25:9: error: 'thisisanerror' undeclared (first use in this function) thisisanerror; ^~~~~~~~~~~~~ conftest.c:25:9: note: each undeclared identifier is reported only once for each function it appears in configure:3831: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__ICC) || defined(__ECC) || defined(__INTEL_COMPILER)) | thisisanerror; | #endif | | ; | return 0; | } configure:3831: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 conftest.c: In function 'main': conftest.c:25:9: error: 'thisisanerror' undeclared (first use in this function) thisisanerror; ^~~~~~~~~~~~~ conftest.c:25:9: note: each undeclared identifier is reported only once for each function it appears in configure:3831: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__xlc__) || defined(__xlC__) || defined(__IBMC__) || defined(__IBMCPP__)) | thisisanerror; | #endif | | ; | return 0; | } configure:3831: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 conftest.c: In function 'main': conftest.c:25:9: error: 'thisisanerror' undeclared (first use in this function) thisisanerror; ^~~~~~~~~~~~~ conftest.c:25:9: note: each undeclared identifier is reported only once for each function it appears in configure:3831: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__PATHCC__) || defined(__PATHSCALE__)) | thisisanerror; | #endif | | ; | return 0; | } configure:3831: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 conftest.c: In function 'main': conftest.c:25:9: error: 'thisisanerror' undeclared (first use in this function) thisisanerror; ^~~~~~~~~~~~~ conftest.c:25:9: note: each undeclared identifier is reported only once for each function it appears in configure:3831: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__clang__)) | thisisanerror; | #endif | | ; | return 0; | } configure:3831: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 conftest.c: In function 'main': conftest.c:25:9: error: 'thisisanerror' undeclared (first use in this function) thisisanerror; ^~~~~~~~~~~~~ conftest.c:25:9: note: each undeclared identifier is reported only once for each function it appears in configure:3831: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(_CRAYC)) | thisisanerror; | #endif | | ; | return 0; | } configure:3831: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 conftest.c: In function 'main': conftest.c:25:9: error: 'thisisanerror' undeclared (first use in this function) thisisanerror; ^~~~~~~~~~~~~ conftest.c:25:9: note: each undeclared identifier is reported only once for each function it appears in configure:3831: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | /* end confdefs.h. */ | | int | main () | { | | #if !(defined(__FUJITSU)) | thisisanerror; | #endif | | ; | return 0; | } configure:3831: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3831: $? = 0 configure:3839: result: gnu configure:3847: checking for gcc option to accept ISO C99 configure:3996: gcc -c -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 conftest.c >&5 configure:3996: $? = 0 configure:4009: result: none needed configure:4117: checking for gcc option to accept ISO Standard C configure:4128: result: none needed configure:4372: checking for a sed that does not truncate output configure:4436: result: /bin/sed configure:4442: checking for grep that handles long lines and -e configure:4500: result: /bin/grep configure:4505: checking for egrep configure:4567: result: /bin/grep -E configure:4755: checking whether gcc is Clang configure:4780: result: no configure:4903: checking whether pthreads work with -pthread configure:4997: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 configure:4997: $? = 0 configure:5006: result: yes configure:5025: checking for joinable pthread attribute configure:5043: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 configure:5043: $? = 0 configure:5051: result: PTHREAD_CREATE_JOINABLE configure:5065: checking whether more special flags are required for pthreads configure:5078: result: no configure:5086: checking for PTHREAD_PRIO_INHERIT configure:5102: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 configure:5102: $? = 0 configure:5111: result: yes configure:5253: checking whether gcc can compile our Altivec/VMX code configure:5285: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 conftest.c:23:10: fatal error: altivec.h: No such file or directory #include ^~~~~~~~~~~ compilation terminated. configure:5285: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define HAVE_PTHREAD 1 | #define HMMER_THREADS 1 | /* end confdefs.h. */ | | #include | #include | int stub_vmx(void) { | vector signed int v1,v2; | union { vector signed int v; int32_t x[4]; } v3; | v1 = vec_splat_s32(6); | v2 = vec_splat_s32(12); | v3.v = vec_add(v1,v2); | return (int) v3.x[0];} | int main(void) { if (stub_vmx() != 18) return 1; else return 0; } | configure:5285: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -maltivec -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 gcc: error: unrecognized command line option '-maltivec'; did you mean '-mglibc'? configure:5285: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define HAVE_PTHREAD 1 | #define HMMER_THREADS 1 | /* end confdefs.h. */ | | #include | #include | int stub_vmx(void) { | vector signed int v1,v2; | union { vector signed int v; int32_t x[4]; } v3; | v1 = vec_splat_s32(6); | v2 = vec_splat_s32(12); | v3.v = vec_add(v1,v2); | return (int) v3.x[0];} | int main(void) { if (stub_vmx() != 18) return 1; else return 0; } | configure:5285: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -faltivec -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 gcc: error: unrecognized command line option '-faltivec' configure:5285: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define HAVE_PTHREAD 1 | #define HMMER_THREADS 1 | /* end confdefs.h. */ | | #include | #include | int stub_vmx(void) { | vector signed int v1,v2; | union { vector signed int v; int32_t x[4]; } v3; | v1 = vec_splat_s32(6); | v2 = vec_splat_s32(12); | v3.v = vec_add(v1,v2); | return (int) v3.x[0];} | int main(void) { if (stub_vmx() != 18) return 1; else return 0; } | configure:5294: result: no configure:5336: checking whether gcc can compile our SSE code configure:5368: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 conftest.c:23:10: fatal error: x86intrin.h: No such file or directory #include ^~~~~~~~~~~~~ compilation terminated. configure:5368: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define HAVE_PTHREAD 1 | #define HMMER_THREADS 1 | /* end confdefs.h. */ | | #include | #include | int stub_sse(void) { | __m128i v1 = _mm_set1_epi32(42); | __m128i v2 = _mm_set1_epi32(86); | union { __m128i v; int32_t x[4]; } v3; | v3.v = _mm_add_epi32(v1, v2); | return (int) v3.x[0]; | } | int main(void) { if (stub_sse() != 128) return 1; else return 0; } | configure:5368: gcc -o conftest -g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.c >&5 gcc: error: unrecognized command line option '-msse2' configure:5368: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HMMER" | #define PACKAGE_TARNAME "hmmer" | #define PACKAGE_VERSION "3.2.1" | #define PACKAGE_STRING "HMMER 3.2.1" | #define PACKAGE_BUGREPORT "sean@eddylab.org" | #define PACKAGE_URL "" | #define HMMER_DATE "June 2018" | #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define HMMER_LICENSE "Freely distributed under the BSD open source license." | #define HMMER_VERSION "3.2.1" | #define HMMER_URL "http://hmmer.org/" | #define EASEL_DATE "June 2018" | #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." | #define EASEL_LICENSE "Freely distributed under the BSD open source license." | #define EASEL_VERSION "0.45h" | #define eslDEBUGLEVEL 0 | #define HAVE_PTHREAD_PRIO_INHERIT 1 | #define HAVE_PTHREAD 1 | #define HMMER_THREADS 1 | /* end confdefs.h. */ | | #include | #include | int stub_sse(void) { | __m128i v1 = _mm_set1_epi32(42); | __m128i v2 = _mm_set1_epi32(86); | union { __m128i v; int32_t x[4]; } v3; | v3.v = _mm_add_epi32(v1, v2); | return (int) v3.x[0]; | } | int main(void) { if (stub_sse() != 128) return 1; else return 0; } | configure:5377: result: no configure:5425: ::::::::::--- no vector instruction set ---:::::::::: configure:5427: HMMER3 requires SSE or VMX vector instructions. configure:5429: Supported platforms are x86 (Intel/AMD) and PowerPC. configure:5431: error: No supported vectorization found for your machine. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=arm-unknown-linux-gnueabi ac_cv_c_compiler_gnu=yes ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set=set ac_cv_env_CFLAGS_value='-g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' ac_cv_env_CPPFLAGS_set=set ac_cv_env_CPPFLAGS_value='-Wdate-time -D_FORTIFY_SOURCE=2' ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_LDFLAGS_set=set ac_cv_env_LDFLAGS_value='-Wl,-z,relro -Wl,-z,now' ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_MPICC_set= ac_cv_env_MPICC_value= ac_cv_env_build_alias_set=set ac_cv_env_build_alias_value=arm-linux-gnueabi ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_host=arm-unknown-linux-gnueabi ac_cv_objext=o ac_cv_path_AR=/usr/bin/ar ac_cv_path_EGREP='/bin/grep -E' ac_cv_path_GREP=/bin/grep ac_cv_path_SED=/bin/sed ac_cv_path_install='/usr/bin/install -c' ac_cv_prog_CPP='gcc -E' ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_cc_c89= ac_cv_prog_cc_c99= ac_cv_prog_cc_g=yes ac_cv_prog_cc_stdc= ax_cv_PTHREAD_CLANG=no ax_cv_PTHREAD_JOINABLE_ATTR=PTHREAD_CREATE_JOINABLE ax_cv_PTHREAD_PRIO_INHERIT=yes ax_cv_PTHREAD_SPECIAL_FLAGS=no ax_cv_c_compiler_vendor=gnu ## ----------------- ## ## Output variables. ## ## ----------------- ## AR='/usr/bin/ar' AVX512_CFLAGS='' AVX_CFLAGS='' CC='gcc' CFLAGS='-g -O2 -fdebug-prefix-map=/build/hmmer-3.2.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' CPP='gcc -E' CPPFLAGS='-Wdate-time -D_FORTIFY_SOURCE=2' DEFS='' EASEL_COPYRIGHT='Copyright (C) 2018 Howard Hughes Medical Institute.' EASEL_DATE='June 2018' EASEL_LICENSE='Freely distributed under the BSD open source license.' EASEL_URL='http://bioeasel.org/' EASEL_VERSION='0.45h' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' GREP='/bin/grep' GROUPHMMERLIBS='' HAVE_GZIP='' HMMERIMPLLIB='' HMMER_COPYRIGHT='Copyright (C) 2018 Howard Hughes Medical Institute.' HMMER_DATE='June 2018' HMMER_ESLDIR='easel' HMMER_LICENSE='Freely distributed under the BSD open source license.' HMMER_URL='http://hmmer.org/' HMMER_VERSION='3.2.1' IMPL_CHOICE='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' LDFLAGS='-Wl,-z,relro -Wl,-z,now' LIBGSL='' LIBOBJS='' LIBS='' LN_S='ln -s' LTLIBOBJS='' MPICC='' MPILIBS='' MPI_BENCHMARKS='' MPI_UTESTS='' NEON_CFLAGS='' OBJEXT='o' PACKAGE_BUGREPORT='sean@eddylab.org' PACKAGE_NAME='HMMER' PACKAGE_STRING='HMMER 3.2.1' PACKAGE_TARNAME='hmmer' PACKAGE_URL='' PACKAGE_VERSION='3.2.1' PATH_SEPARATOR=':' PTHREAD_CC='gcc' PTHREAD_CFLAGS='-pthread' PTHREAD_LIBS='' RANLIB='ranlib' SED='/bin/sed' SHELL='/bin/bash' SSE4_CFLAGS='' SSE_CFLAGS='' VMX_CFLAGS='' ac_ct_CC='gcc' ax_pthread_config='' bindir='${exec_prefix}/bin' build='arm-unknown-linux-gnueabi' build_alias='arm-linux-gnueabi' build_cpu='arm' build_os='linux-gnueabi' build_vendor='unknown' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host='arm-unknown-linux-gnueabi' host_alias='' host_cpu='arm' host_os='linux-gnueabi' host_vendor='unknown' htmldir='${docdir}' includedir='${prefix}/include' infodir='${prefix}/share/info' libdir='${prefix}/lib/arm-linux-gnueabi' libexecdir='${prefix}/lib/arm-linux-gnueabi' localedir='${datarootdir}/locale' localstatedir='/var' mandir='${prefix}/share/man' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/usr' program_transform_name='s,x,x,' psdir='${docdir}' runstatedir='/run' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "HMMER" #define PACKAGE_TARNAME "hmmer" #define PACKAGE_VERSION "3.2.1" #define PACKAGE_STRING "HMMER 3.2.1" #define PACKAGE_BUGREPORT "sean@eddylab.org" #define PACKAGE_URL "" #define HMMER_DATE "June 2018" #define HMMER_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." #define HMMER_LICENSE "Freely distributed under the BSD open source license." #define HMMER_VERSION "3.2.1" #define HMMER_URL "http://hmmer.org/" #define EASEL_DATE "June 2018" #define EASEL_COPYRIGHT "Copyright (C) 2018 Howard Hughes Medical Institute." #define EASEL_LICENSE "Freely distributed under the BSD open source license." #define EASEL_VERSION "0.45h" #define eslDEBUGLEVEL 0 #define HAVE_PTHREAD_PRIO_INHERIT 1 #define HAVE_PTHREAD 1 #define HMMER_THREADS 1 configure: exit 1 dh_auto_configure: ./configure --build=arm-linux-gnueabi --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --libexecdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads returned exit code 1 make[1]: *** [debian/rules:27: override_dh_auto_configure] Error 2 make[1]: Leaving directory '/build/hmmer-3.2.1+dfsg' make: *** [debian/rules:13: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 I: Terminate timeout process I: copying local configuration /usr/lib/pbuilder/pbuilder-modules: line 1: 32154 Terminated ( : Timeout process; sleep "${TIMEOUT_TIME}"; log.i "Terminating build process due to timeout "; kill "${BUILD_PID}" || true ) E: Failed autobuilding of package I: user script /chroot/rebuildd/pbuilder/11096/tmp/hooks/C01kill-gpg-agent starting Found other processes running as uid 1234, killing them: 738 /tmp/hooks/C01kill-gpg-agent: 22: kill: No such process I: user script /chroot/rebuildd/pbuilder/11096/tmp/hooks/C01kill-gpg-agent finished I: unmounting /sys filesystem I: unmounting /proc filesystem I: unmounting /dev/pts filesystem I: unmounting /dev filesystem I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env  I: removing directory /chroot/rebuildd/pbuilder/11096 and its subdirectories FAILED to build: 1