Date: Sat, 23 Dec 2017 02:20:47 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/hmmer] Failed for hmmer-3.1b2 in package Message-ID: <201712230220.vBN2KleZ030634@beefy8.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: mzaki@niid.go.jp Last committer: wen@FreeBSD.org Ident: $FreeBSD: head/biology/hmmer/Makefile 453972 2017-11-11 12:51:52Z wen $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p456877_s327051/logs/hmmer-3.1b2.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p456877_s327051 Log: =>> Building biology/hmmer build started at Sat Dec 23 02:18:49 UTC 2017 port directory: /usr/ports/biology/hmmer package name: hmmer-3.1b2 building for: FreeBSD head-armv6-default-job-04 12.0-CURRENT FreeBSD 12.0-CURRENT 1200054 arm maintained by: mzaki@niid.go.jp Makefile ident: $FreeBSD: head/biology/hmmer/Makefile 453972 2017-11-11 12:51:52Z wen $ Poudriere version: 3.2.3-16-g77e43413 Host OSVERSION: 1200052 Jail OSVERSION: 1200054 Job Id: 04 !!! Jail is newer than host. (Jail: 1200054, Host: 1200052) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200054 UNAME_v=FreeBSD 12.0-CURRENT 1200054 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk OLDPWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root P_PYTHON_MAJOR_VER=2 POUDRIERE_VERSION=3.2.3-16-g77e43413 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for hmmer-3.1b2: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples TEST=off: Build and/or run tests ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- mzaki@niid.go.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hmmer/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hmmer/work HOME=/wrkdirs/usr/ports/biology/hmmer/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hmmer/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hmmer/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hmmer/work HOME=/wrkdirs/usr/ports/biology/hmmer/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hmmer/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=armv6 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=12.0 OSVERSION=1200054 PYTHONBASE=/usr/local UID=0 _OSRELEASE=12.0-CURRENT #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> hmmer-3.1b2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.3_1.txz [head-armv6-default-job-04] Installing pkg-1.10.3_1... [head-armv6-default-job-04] Extracting pkg-1.10.3_1: .......... done ===> hmmer-3.1b2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hmmer-3.1b2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.1b2 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.1b2 for building => SHA256 Checksum OK for hmmer-3.1b2.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hmmer-3.1b2 for building ===> Extracting for hmmer-3.1b2 => SHA256 Checksum OK for hmmer-3.1b2.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for hmmer-3.1b2 ===> Applying FreeBSD patches for hmmer-3.1b2 =========================================================================== =======================<phase: build-depends >============================ <snip> fm_general.c:172:42: note: use function 'llabs' instead interval->upper = interval_bk.upper = abs(fm->C[c+1])-1; ^~~ llabs fm_general.c:197:21: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->lower = abs(fm->C[(int)c]) + count1; ^ fm_general.c:197:21: note: use function 'llabs' instead interval->lower = abs(fm->C[(int)c]) + count1; ^~~ llabs fm_general.c:198:21: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->upper = abs(fm->C[(int)c]) + count2 - 1; ^ fm_general.c:198:21: note: use function 'llabs' instead interval->upper = abs(fm->C[(int)c]) + count2 - 1; ^~~ llabs fm_general.c:220:22: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->lower = abs(fm->C[(int)c]); ^ fm_general.c:220:22: note: use function 'llabs' instead interval->lower = abs(fm->C[(int)c]); ^~~ llabs fm_general.c:221:22: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->upper = abs(fm->C[(int)c+1])-1; ^ fm_general.c:221:22: note: use function 'llabs' instead interval->upper = abs(fm->C[(int)c+1])-1; ^~~ llabs fm_general.c:572:13: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] prevC = abs(C[i]); ^ fm_general.c:572:13: note: use function 'llabs' instead prevC = abs(C[i]); ^~~ llabs 9 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o fm_sse.o -c fm_sse.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o fm_ssv.o -c fm_ssv.c fm_ssv.c:136:10: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] j += abs(fmf->C[c]); ^ fm_ssv.c:136:10: note: use function 'llabs' instead j += abs(fmf->C[c]); ^~~ llabs fm_ssv.c:464:65: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval_f1.upper = interval_f2.upper = interval_bk.upper = abs(fmf->C[i+1])-1; ^ fm_ssv.c:464:65: note: use function 'llabs' instead interval_f1.upper = interval_f2.upper = interval_bk.upper = abs(fmf->C[i+1])-1; ^~~ llabs 2 warnings generated. /usr/bin/ar -r libhmmer.a build.o cachedb.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_fwdback_chk.o generic_fwdback_banded.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmlogo.o hmmdmstr.o hmmdwrkr.o hmmdutils.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_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hmm.o p7_hmmcache.o p7_hmmfile.o p7_hmmwindow.o p7_null3.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o p7_scoredata.o hmmpgmd2msa.o fm_alphabet.o fm_general.o fm_sse.o fm_ssv.o > /dev/null 2>&1 /usr/local/bin/gmake -C impl_dummy libhmmer-impl.stamp gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy' /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c decoding.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c fwdback.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c io.c io.c:165:12: warning: comparison of array 'hfp->errbuf' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (hfp->errbuf != NULL) hfp->errbuf[0] = '\0'; ~~~~~^~~~~~ ~~~~ io.c:278:12: warning: comparison of array 'hfp->errbuf' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (hfp->errbuf != NULL) hfp->errbuf[0] = '\0'; ~~~~~^~~~~~ ~~~~ 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c msvfilter.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c null2.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c optacc.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c stotrace.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c vitfilter.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c p7_omx.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c p7_oprofile.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -c mpi.c /usr/bin/ar -r ../libhmmer.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 > /dev/null 2>&1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy' /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmalign.o -c hmmalign.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmemit.o -c hmmemit.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpress.o -c hmmpress.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmscan.o -c hmmscan.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsim.o -c hmmsim.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmstat.o -c hmmstat.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o phmmer.o -c phmmer.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmer.o -c nhmmer.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c nhmmscan.c:671:9: warning: implicit declaration of function 'p7_oprofile_UpdateVitEmissionScores' is invalid in C99 [-Wimplicit-function-declaration] p7_oprofile_UpdateVitEmissionScores(om, info->bg, info->fwd_emissions, info->scores); ^ nhmmscan.c:672:9: warning: implicit declaration of function 'p7_oprofile_UpdateMSVEmissionScores' is invalid in C99 [-Wimplicit-function-declaration] p7_oprofile_UpdateMSVEmissionScores(om, info->bg, info->fwd_emissions, info->scores); ^ 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmc2.o -c hmmc2.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c makehmmerdb.c:642:33: warning: comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if (meta->inv_alph[c] == -1) { ~~~~~~~~~~~~~~~~~ ^ ~~ makehmmerdb.c:655:38: warning: comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] } else if (meta->inv_alph[c] == -1) { ~~~~~~~~~~~~~~~~~ ^ ~~ 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c hmmerfm-exactmatch.c:158:12: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] j += abs(fm->C[c]); ^ hmmerfm-exactmatch.c:158:12: note: use function 'llabs' instead j += abs(fm->C[c]); ^~~ llabs 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L./impl_dummy -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src' gmake -C profmark all gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/profmark' /nxb-bin/usr/bin/cc -I../easel -I../easel -I../src -I../src -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm /nxb-bin/usr/bin/cc -I../easel -I../easel -I../src -I../src -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c /nxb-bin/usr/bin/cc -O2 -pipe -fno-strict-aliasing -D_THREAD_SAFE -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/profmark' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2' =========================================================================== =======================<phase: run-depends >============================ =========================================================================== =======================<phase: stage >============================ ===> Staging for hmmer-3.1b2 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2' /usr/bin/install -c -d /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/bin /usr/bin/install -c -d /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/lib /usr/bin/install -c -d /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include /usr/bin/install -c -d /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/man/man1 /usr/bin/install -c -d /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/share/doc/hmmer gmake -C src install gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src' /usr/local/bin/gmake -C impl_dummy install gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy' for file in impl_dummy.h; do \ /usr/bin/install -c -m 0644 ./$file /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/ ;\ done gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src/impl_dummy' for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan hmmpgmd hmmc2 makehmmerdb hmmerfm-exactmatch; do \ /usr/bin/install -c -m 0755 $file /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/bin/ ;\ done /usr/bin/install -c -m 0755 libhmmer.a /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/lib/ for file in hmmer.h cachedb.h p7_gbands.h p7_gmxb.h p7_gmxchk.h p7_hmmcache.h; do \ /usr/bin/install -c -m 0644 ./$file /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/ ;\ done /usr/bin/install -c -m 0644 p7_config.h /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/ ;\ gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/src' gmake -C documentation install gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation' /usr/local/bin/gmake -C man install gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation/man' for file in hmmer hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \ /usr/bin/install -c -m 0755 ./$file.man /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/man/man1/${file}.1 ;\ done gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation/man' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/documentation' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2' install -m 0644 /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/COPYRIGHT /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/Userguide.pdf /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/share/doc/hmmer install -m 0644 /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/7LESS_DROME /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/HBB_HUMAN /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/MADE1.hmm /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/MADE1.out /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/MADE1.sto /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/Pkinase.hmm /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/Pkinase.sto /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/dna_target.fa /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/fn3.hmm /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/fn3.out /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/fn3.sto /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins4.hmm /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins4.out /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins4.sto /w rkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/globins45.fa /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3f /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3i /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3m /wrkdirs/usr/ports/biology/hmmer/work/hmmer-3.1b2/tutorial/minifam.h3p /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/share/examples/hmmer ====> Compressing man pages (compress-man) =========================================================================== =======================<phase: package >============================ ===> Building package for hmmer-3.1b2 pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hmmer/work/stage/usr/local/include/impl_sse.h:No such file or directory *** Error code 1 Stop. make: stopped in /usr/ports/biology/hmmer
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