=> Building biology/hmmer build started at Wed Oct 5 05:36:24 PDT 2016 port directory: /usr/ports/biology/hmmer building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: bacon4000@gmail.com ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../09//usr/ports/biology/hmmer/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=hmmer-3.0_1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for hmmer-3.0_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --enable-threads --enable-sse --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/biology/hmmer XDG_CONFIG_HOME=/wrkdirs/biology/hmmer HOME=/wrkdirs/biology/hmmer TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/hmmer XDG_CONFIG_HOME=/wrkdirs/biology/hmmer HOME=/wrkdirs/biology/hmmer TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.20 PROFILE="@comment " DOCSDIR="share/doc/hmmer" EXAMPLESDIR="share/examples/hmmer" DATADIR="share/hmmer" WWWDIR="www/hmmer" ETCDIR="etc/hmmer" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hmmer DOCSDIR=/usr/local/share/doc/hmmer EXAMPLESDIR=/usr/local/share/examples/hmmer WWWDIR=/usr/local/www/hmmer ETCDIR=/usr/local/etc/hmmer --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> hmmer-3.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> hmmer-3.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hmmer-3.0_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.0_1 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.0_1 for building => SHA256 Checksum OK for hmmer-3.0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.0_1 for building ===> Extracting for hmmer-3.0_1 => SHA256 Checksum OK for hmmer-3.0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for hmmer-3.0_1 =========================================================================== =================================================== ===> hmmer-3.0_1 depends on package: perl5>=5.20<5.21 - not found ===> Installing existing package /packages/All/perl5-5.20.3_15.txz Installing perl5-5.20.3_15... Extracting perl5-5.20.3_15: .......... done Message from perl5-5.20.3_15: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> hmmer-3.0_1 depends on package: perl5>=5.20<5.21 - found ===> Returning to build of hmmer-3.0_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for hmmer-3.0_1 configure: loading site script /usr/ports/Templates/config.site configure: Configuring HMMER for your system. checking build system type... x86_64-portbld-dragonfly4.7 checking host system type... x86_64-portbld-dragonfly4.7 configure: Full HMMER source distribution - using full configuration checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for C compiler vendor... gnu checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking for gcc... (cached) cc checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking how to run the C preprocessor... cpp checking for C compiler vendor... (cached) gnu checking for cc option to accept ISO C99... none needed checking for cc option to accept ISO Standard C... (cached) none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether your make is GNU make... nope, assuming sysv make. checking whether C compiler accepts -msse2... yes checking compiler support for sse2 cast functions... yes checking whether SSE2 is supported... yes checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes configure: Activating Intel/AMD SSE optimized DP implementation checking compiler support --start-group... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking sys/sysctl.h usability... yes checking sys/sysctl.h presence... yes checking for sys/sysctl.h... yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking endian.h usability... no checking endian.h presence... no checking for endian.h... no checking whether byte ordering is bigendian... no checking for uint8_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint64_t... (cached) yes checking for off_t... (cached) yes checking for mkstemp... (cached) yes checking for popen... yes checking for strcasecmp... (cached) yes checking for times... yes checking for getpid... (cached) yes checking for sysctl... yes checking for sysconf... (cached) yes checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_sse/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating Makefile config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: linking src/impl_sse to src/impl HMMER configuration: compiler: cc -pipe -O2 -fno-strict-aliasing -msse2 -pthread linker: libraries: DP implementation: sse =========================================================================== =================================================== ===> Building for hmmer-3.0_1 --- easel_lib --- --- impl_lib --- --- hmmer_lib --- --- impl_lib --- cd src/impl_sse; /usr/bin/make libhmmerimpl.a --- easel_lib --- cd easel; /usr/bin/make libeasel.a --- hmmer_lib --- cd src; /usr/bin/make libhmmer.a --- build.o --- --- emit.o --- --- errors.o --- --- build.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o build.o -c build.c --- emit.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o emit.o -c emit.c --- errors.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o errors.o -c errors.c --- easel_lib --- --- easel.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o easel.o -c easel.c --- impl_lib --- --- decoding.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o decoding.o -c decoding.c --- easel_lib --- --- esl_alphabet.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_alphabet.o -c esl_alphabet.c --- esl_cluster.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_cluster.o -c esl_cluster.c --- esl_dirichlet.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_dirichlet.o -c esl_dirichlet.c --- impl_lib --- --- fwdback.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o fwdback.o -c fwdback.c --- hmmer_lib --- --- evalues.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o evalues.o -c evalues.c --- impl_lib --- --- io.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o io.o -c io.c --- hmmer_lib --- --- eweight.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o eweight.o -c eweight.c --- generic_decoding.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_decoding.o -c generic_decoding.c --- generic_fwdback.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c --- impl_lib --- --- msvfilter.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o msvfilter.o -c msvfilter.c --- null2.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o null2.o -c null2.c --- optacc.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o optacc.o -c optacc.c --- easel_lib --- --- esl_distance.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_distance.o -c esl_distance.c --- hmmer_lib --- --- generic_null2.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_null2.o -c generic_null2.c --- impl_lib --- --- stotrace.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o stotrace.o -c stotrace.c --- hmmer_lib --- --- generic_msv.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_msv.o -c generic_msv.c --- easel_lib --- --- esl_dmatrix.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_dmatrix.o -c esl_dmatrix.c --- impl_lib --- --- vitfilter.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o vitfilter.o -c vitfilter.c --- hmmer_lib --- --- generic_optacc.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_optacc.o -c generic_optacc.c --- impl_lib --- --- p7_omx.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o p7_omx.o -c p7_omx.c --- easel_lib --- --- esl_exponential.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_exponential.o -c esl_exponential.c --- esl_fileparser.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_fileparser.o -c esl_fileparser.c --- hmmer_lib --- --- generic_stotrace.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c --- generic_viterbi.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c --- easel_lib --- --- esl_gamma.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_gamma.o -c esl_gamma.c --- esl_getopts.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_getopts.o -c esl_getopts.c --- hmmer_lib --- --- generic_vtrace.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c --- easel_lib --- --- esl_gev.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_gev.o -c esl_gev.c --- esl_gumbel.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_gumbel.o -c esl_gumbel.c --- hmmer_lib --- --- h2_io.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o h2_io.o -c h2_io.c --- heatmap.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o heatmap.o -c heatmap.c --- easel_lib --- --- esl_histogram.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_histogram.o -c esl_histogram.c --- impl_lib --- --- p7_oprofile.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o p7_oprofile.o -c p7_oprofile.c --- hmmer_lib --- --- hmmer.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmer.o -c hmmer.c --- logsum.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o logsum.o -c logsum.c --- modelconfig.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o modelconfig.o -c modelconfig.c --- modelstats.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o modelstats.o -c modelstats.c --- impl_lib --- --- mpi.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -o mpi.o -c mpi.c --- hmmer_lib --- --- mpisupport.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o mpisupport.o -c mpisupport.c --- seqmodel.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o seqmodel.o -c seqmodel.c --- tracealign.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o tracealign.o -c tracealign.c --- easel_lib --- --- esl_hmm.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_hmm.o -c esl_hmm.c --- hmmer_lib --- --- p7_alidisplay.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c --- easel_lib --- --- esl_hyperexp.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_hyperexp.o -c esl_hyperexp.c --- hmmer_lib --- --- p7_bg.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_bg.o -c p7_bg.c --- easel_lib --- --- esl_keyhash.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_keyhash.o -c esl_keyhash.c --- hmmer_lib --- --- p7_builder.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_builder.o -c p7_builder.c --- easel_lib --- --- esl_minimizer.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_minimizer.o -c esl_minimizer.c --- esl_mixgev.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_mixgev.o -c esl_mixgev.c --- hmmer_lib --- --- p7_domaindef.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c --- easel_lib --- --- esl_mpi.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_mpi.o -c esl_mpi.c --- esl_msa.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_msa.o -c esl_msa.c --- esl_msacluster.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_msacluster.o -c esl_msacluster.c --- hmmer_lib --- --- p7_gmx.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_gmx.o -c p7_gmx.c --- easel_lib --- --- esl_msashuffle.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_msashuffle.o -c esl_msashuffle.c --- hmmer_lib --- --- p7_hmm.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_hmm.o -c p7_hmm.c --- easel_lib --- --- esl_msaweight.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_msaweight.o -c esl_msaweight.c --- esl_normal.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_normal.o -c esl_normal.c --- impl_lib --- --- libhmmerimpl.a --- /usr/bin/ar rcv libhmmerimpl.a decoding.o fwdback.o io.o msvfilter.o null2.o optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o a - decoding.o a - fwdback.o a - io.o a - msvfilter.o a - null2.o a - optacc.o a - stotrace.o a - vitfilter.o a - p7_omx.o a - p7_oprofile.o a - mpi.o ranlib libhmmerimpl.a chmod 644 libhmmerimpl.a --- hmmer_lib --- --- p7_hmmfile.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c --- easel_lib --- --- esl_paml.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_paml.o -c esl_paml.c --- esl_random.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_random.o -c esl_random.c --- esl_randomseq.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_randomseq.o -c esl_randomseq.c --- hmmer_lib --- --- p7_pipeline.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c --- p7_prior.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_prior.o -c p7_prior.c --- p7_profile.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_profile.o -c p7_profile.c --- p7_spensemble.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c --- p7_tophits.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_tophits.o -c p7_tophits.c --- p7_trace.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o p7_trace.o -c p7_trace.c --- easel_lib --- --- esl_ratematrix.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_ratematrix.o -c esl_ratematrix.c --- esl_regexp.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_regexp.o -c esl_regexp.c --- esl_rootfinder.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_rootfinder.o -c esl_rootfinder.c --- esl_scorematrix.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_scorematrix.o -c esl_scorematrix.c --- esl_sq.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_sq.o -c esl_sq.c --- hmmer_lib --- --- libhmmer.a --- /usr/bin/ar rcv libhmmer.a build.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmer.o logsum.o modelconfig.o modelstats.o mpisupport.o seqmodel.o tracealign.o p7_alidisplay.o p7_bg.o p7_builder.o p7_domaindef.o p7_gmx.o p7_hmm.o p7_hmmfile.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o a - build.o a - emit.o a - errors.o a - evalues.o a - eweight.o a - generic_decoding.o a - generic_fwdback.o a - generic_null2.o a - generic_msv.o a - generic_optacc.o a - generic_stotrace.o a - generic_viterbi.o a - generic_vtrace.o a - h2_io.o a - heatmap.o a - hmmer.o a - logsum.o a - modelconfig.o a - modelstats.o a - mpisupport.o a - seqmodel.o a - tracealign.o a - p7_alidisplay.o a - p7_bg.o a - p7_builder.o a - p7_domaindef.o a - p7_gmx.o a - p7_hmm.o a - p7_hmmfile.o a - p7_pipeline.o a - p7_prior.o a - p7_profile.o a - p7_spensemble.o a - p7_tophits.o a - p7_trace.o ranlib libhmmer.a chmod 644 libhmmer.a --- easel_lib --- --- esl_sqio.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_sqio.o -c esl_sqio.c --- esl_sqio_ascii.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_sqio_ascii.o -c esl_sqio_ascii.c --- esl_sqio_ncbi.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_sqio_ncbi.o -c esl_sqio_ncbi.c --- esl_sse.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_sse.o -c esl_sse.c --- esl_ssi.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_ssi.o -c esl_ssi.c --- esl_stack.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_stack.o -c esl_stack.c --- esl_stats.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_stats.o -c esl_stats.c --- esl_stopwatch.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_stopwatch.o -c esl_stopwatch.c --- esl_stretchexp.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_stretchexp.o -c esl_stretchexp.c --- esl_threads.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_threads.o -c esl_threads.c --- esl_tree.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_tree.o -c esl_tree.c --- esl_vectorops.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_vectorops.o -c esl_vectorops.c --- esl_vmx.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_vmx.o -c esl_vmx.c --- esl_weibull.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_weibull.o -c esl_weibull.c --- esl_workqueue.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_workqueue.o -c esl_workqueue.c --- esl_wuss.o --- cc -I. -I. -pipe -O2 -fno-strict-aliasing -pthread -msse2 -o esl_wuss.o -c esl_wuss.c --- libeasel.a --- /usr/bin/ar rcv libeasel.a easel.o esl_alphabet.o esl_cluster.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_getopts.o esl_gev.o esl_gumbel.o esl_histogram.o esl_hmm.o esl_hyperexp.o esl_keyhash.o esl_minimizer.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_random.o esl_randomseq.o esl_ratematrix.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sqio_ascii.o esl_sqio_ncbi.o esl_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_threads.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_workqueue.o esl_wuss.o a - easel.o a - esl_alphabet.o a - esl_cluster.o a - esl_dirichlet.o a - esl_distance.o a - esl_dmatrix.o a - esl_exponential.o a - esl_fileparser.o a - esl_gamma.o a - esl_getopts.o a - esl_gev.o a - esl_gumbel.o a - esl_histogram.o a - esl_hmm.o a - esl_hyperexp.o a - esl_keyhash.o a - esl_minimizer.o a - esl_mixgev.o a - esl_mpi.o a - esl_msa.o a - esl_msacluster.o a - esl_msashuffle.o a - esl_msaweight.o a - esl_normal.o a - esl_paml.o a - esl_random.o a - esl_randomseq.o a - esl_ratematrix.o a - esl_regexp.o a - esl_rootfinder.o a - esl_scorematrix.o a - esl_sq.o a - esl_sqio.o a - esl_sqio_ascii.o a - esl_sqio_ncbi.o a - esl_sse.o a - esl_ssi.o a - esl_stack.o a - esl_stats.o a - esl_stopwatch.o a - esl_stretchexp.o a - esl_threads.o a - esl_tree.o a - esl_vectorops.o a - esl_vmx.o a - esl_weibull.o a - esl_workqueue.o a - esl_wuss.o ranlib libeasel.a chmod 644 libeasel.a --- easel_progs --- --- hmmer_progs --- --- profmark_progs --- --- easel_progs --- cd easel; /usr/bin/make easel_progs --- hmmer_progs --- cd src; /usr/bin/make hmmer_progs --- profmark_progs --- cd profmark; /usr/bin/make profmark_progs --- create-profmark.o --- --- rocplot.o --- --- easel_progs --- --- easel_progs --- --- profmark_progs --- --- create-profmark.o --- cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c --- rocplot.o --- cc -I../easel -I../easel -I../src -I../src -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c --- easel_progs --- cd miniapps; /usr/bin/make easel_progs --- hmmer_progs --- --- hmmalign.o --- --- hmmbuild.o --- --- hmmalign.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmalign.o -c hmmalign.c --- hmmbuild.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c --- easel_progs --- --- esl-afetch.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-afetch.o -c esl-afetch.c --- esl-alimanip.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimanip.o -c esl-alimanip.c --- profmark_progs --- --- create-profmark --- cc -pipe -O2 -fno-strict-aliasing -DHAVE_CONFIG_H -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm --- rocplot --- cc -pipe -O2 -fno-strict-aliasing -DHAVE_CONFIG_H -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm --- easel_progs --- --- esl-alimap.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimap.o -c esl-alimap.c --- hmmer_progs --- --- hmmconvert.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c --- hmmemit.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmemit.o -c hmmemit.c --- hmmfetch.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c --- hmmpress.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmpress.o -c hmmpress.c --- hmmscan.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmscan.o -c hmmscan.c --- hmmsearch.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c --- hmmsim.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmsim.o -c hmmsim.c --- hmmstat.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o hmmstat.o -c hmmstat.c --- jackhmmer.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c --- phmmer.o --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -I../easel -I../easel -I. -I. -o phmmer.o -c phmmer.c --- hmmconvert --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmconvert hmmconvert.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmalign --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmalign hmmalign.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmemit --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmemit hmmemit.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmpress --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmpress hmmpress.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmfetch --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmfetch hmmfetch.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmbuild --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmbuild hmmbuild.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmscan --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmscan hmmscan.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmstat --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmstat hmmstat.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmsim --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmsim hmmsim.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- hmmsearch --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o hmmsearch hmmsearch.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- easel_progs --- --- esl-alimask.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimask.o -c esl-alimask.c --- hmmer_progs --- --- phmmer --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o phmmer phmmer.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- easel_progs --- --- esl-alimerge.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alimerge.o -c esl-alimerge.c --- esl-alistat.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-alistat.o -c esl-alistat.c --- hmmer_progs --- --- jackhmmer --- cc -pipe -O2 -fno-strict-aliasing -pthread -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -o jackhmmer jackhmmer.o -Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group -leasel -lm --- easel_progs --- --- esl-cluster.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-cluster.o -c esl-cluster.c --- esl-compalign.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compalign.o -c esl-compalign.c --- esl-compstruct.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-compstruct.o -c esl-compstruct.c --- esl-construct.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-construct.o -c esl-construct.c --- esl-histplot.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-histplot.o -c esl-histplot.c --- esl-mask.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-mask.o -c esl-mask.c --- esl-reformat.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-reformat.o -c esl-reformat.c --- esl-selectn.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-selectn.o -c esl-selectn.c --- esl-seqstat.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-seqstat.o -c esl-seqstat.c --- esl-sfetch.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-sfetch.o -c esl-sfetch.c --- esl-shuffle.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-shuffle.o -c esl-shuffle.c --- esl-ssdraw.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-ssdraw.o -c esl-ssdraw.c --- esl-weight.o --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -I. -I.. -I. -I./.. -o esl-weight.o -c esl-weight.c --- esl-afetch --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-afetch esl-afetch.o -leasel -lm --- esl-alimap --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimap esl-alimap.o -leasel -lm --- esl-cluster --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-cluster esl-cluster.o -leasel -lm --- esl-compalign --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-compalign esl-compalign.o -leasel -lm --- esl-alistat --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-alistat esl-alistat.o -leasel -lm --- esl-compstruct --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-compstruct esl-compstruct.o -leasel -lm --- esl-alimask --- --- esl-histplot --- --- esl-alimask --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimask esl-alimask.o -leasel -lm --- esl-histplot --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-histplot esl-histplot.o -leasel -lm --- esl-mask --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-mask esl-mask.o -leasel -lm --- esl-reformat --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-reformat esl-reformat.o -leasel -lm --- esl-selectn --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-selectn esl-selectn.o -leasel -lm --- esl-seqstat --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-seqstat esl-seqstat.o -leasel -lm --- esl-alimanip --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimanip esl-alimanip.o -leasel -lm --- esl-sfetch --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-sfetch esl-sfetch.o -leasel -lm --- esl-shuffle --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-shuffle esl-shuffle.o -leasel -lm --- esl-weight --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-weight esl-weight.o -leasel -lm --- esl-alimerge --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimerge esl-alimerge.o -leasel -lm --- esl-construct --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-construct esl-construct.o -leasel -lm --- esl-ssdraw --- cc -pipe -O2 -fno-strict-aliasing -msse2 -DHAVE_CONFIG_H -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm =========================================================================== =================================================== ===> hmmer-3.0_1 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== ===> Staging for hmmer-3.0_1 ===> Generating temporary packing list cd easel; /usr/bin/make libeasel.a `libeasel.a' is up to date. cd src/impl_sse; /usr/bin/make libhmmerimpl.a `libhmmerimpl.a' is up to date. cd src; /usr/bin/make libhmmer.a `libhmmer.a' is up to date. cd easel; /usr/bin/make easel_progs cd miniapps; /usr/bin/make easel_progs cd src; /usr/bin/make hmmer_progs cd profmark; /usr/bin/make profmark_progs cd profmark; /usr/bin/make profmark_progs mkdir -p /wrkdirs/biology/hmmer/stage/usr/local/bin for file in hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer; do cp src/$file /wrkdirs/biology/hmmer/stage/usr/local/bin/; done (cd /wrkdirs/biology/hmmer/hmmer-3.0/documentation/man; for i in *.man; do install -m 444 $i /wrkdirs/biology/hmmer/stage/usr/local/man/man1/`echo $i|/usr/bin/sed 's/.man/.1/'`; done) install -m 0644 /wrkdirs/biology/hmmer/hmmer-3.0/COPYRIGHT /wrkdirs/biology/hmmer/hmmer-3.0/INSTALL /wrkdirs/biology/hmmer/hmmer-3.0/LICENSE /wrkdirs/biology/hmmer/hmmer-3.0/Userguide.pdf /wrkdirs/biology/hmmer/stage/usr/local/share/doc/hmmer install -m 0644 /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/7LESS_DROME /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/Pkinase.sto /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/fn3.sto /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/globins4.sto /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/minifam.h3f /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/minifam.h3p /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/HBB_HUMAN /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/fn3.hmm /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/globins4.hmm /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/globins45.fa /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/minifam.h3i /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/Pkinase.hmm /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/fn3.out /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/globins4.out /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/minifam /wrkdirs/biology/hmmer/hmmer-3.0/tutorial/minifam.h3m /wrkdirs/biology/hmmer/stage/usr/local/share/examples/hmmer ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for hmmer-3.0_1 file sizes/checksums [48]: . done packing files [48]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for hmmer-3.0_1 build of biology/hmmer ended at Wed Oct 5 05:37:34 PDT 2016 build time: 00:01:10