=> Building biology/fasta3 Started : Thursday, 7 MAR 2019 at 18:14:05 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for fasta3-36.3.8: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/fasta3 XDG_CONFIG_HOME=/construction/biology/fasta3 HOME=/construction/biology/fasta3 TMPDIR="/tmp" PATH=/construction/biology/fasta3/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- THR_LIBS="-pthread" XDIR="/construction/biology/fasta3/stage/usr/local/bin" FASTA_HOST="$(/usr/bin/uname -n)" XDG_DATA_HOME=/construction/biology/fasta3 XDG_CONFIG_HOME=/construction/biology/fasta3 HOME=/construction/biology/fasta3 TMPDIR="/tmp" PATH=/construction/biology/fasta3/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/fasta3/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- VER="36" PORTDOCS="" PORTEXAMPLES="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/fasta3" EXAMPLESDIR="share/examples/fasta3" DATADIR="share/fasta3" WWWDIR="www/fasta3" ETCDIR="etc/fasta3" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fasta3 DOCSDIR=/usr/local/share/doc/fasta3 EXAMPLESDIR=/usr/local/share/examples/fasta3 WWWDIR=/usr/local/www/fasta3 ETCDIR=/usr/local/etc/fasta3 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License Fasta accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> fasta3-36.3.8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> fasta3-36.3.8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fasta3-36.3.8 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License Fasta accepted by the user ===> Fetching all distfiles required by fasta3-36.3.8 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License Fasta accepted by the user ===> Fetching all distfiles required by fasta3-36.3.8 for building => SHA256 Checksum OK for fasta3/2014-01-29/fasta-36.3.8.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License Fasta accepted by the user ===> Fetching all distfiles required by fasta3-36.3.8 for building ===> Extracting for fasta3-36.3.8 => SHA256 Checksum OK for fasta3/2014-01-29/fasta-36.3.8.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for fasta3-36.3.8 ===> Applying ports patches for fasta3-36.3.8 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for fasta3-36.3.8 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for fasta3-36.3.8 --- init_sw.o --- --- lwm_align.o --- --- calcons_sw.o --- --- comp_mlib9.o --- --- compacc2_s.o --- --- init_sw.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DSSEARCH initfa.c -o init_sw.o --- lwm_align.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c wm_align.c -o lwm_align.o --- calcons_sw.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DSSEARCH -c cal_cons2.c -o calcons_sw.o --- comp_mlib9.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o --- compacc2_s.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_MLIB -c compacc2e.c -o compacc2_s.o --- calcons_sw.o --- cal_cons2.c: In function 'init_update_data': cal_cons2.c:894:1: warning: type of 'show_code' defaults to 'int' [-Wimplicit-int] init_update_data(show_code) { ^~~~~~~~~~~~~~~~ --- lshowalign.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DLALIGN -c mshowalign2.c -o lshowalign.o In file included from mshowalign2.c:33: mshowalign2.c: In function 'showalign': defs.h:25:41: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] #define SAFE_STRNCPY(dest,src,dest_len) strncpy(dest,src,dest_len); dest[dest_len-1]='\0' ^~~~~~~~~~~~~~~~~~~~~~~~~~ mshowalign2.c:561:8: note: in expansion of macro 'SAFE_STRNCPY' SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); ^~~~~~~~~~~~ --- init_sw.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- compacc2_s.o --- compacc2e.c: In function 'next_annot_entry': compacc2e.c:1990:2: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- init_lal.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DLALIGN initfa.c -o init_lal.o --- droplal2.o --- cc -DLALIGN -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropgsw2.c -o droplal2.o --- calcons_la.o --- cc -DLALIGN -DLCAL_CONS -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c cal_cons2.c -o calcons_la.o cal_cons2.c: In function 'init_update_data': cal_cons2.c:894:1: warning: type of 'show_code' defaults to 'int' [-Wimplicit-int] init_update_data(show_code) { ^~~~~~~~~~~~~~~~ --- init_fs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS initfa.c -o init_fs.o --- init_fx.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTX initfa.c -o init_fx.o --- init_tfx.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTX -DTFAST initfa.c -o init_tfx.o --- init_lal.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- drop_tfx.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST dropfx2.c -o drop_tfx.o dropfx2.c: In function 'init_update_data': dropfx2.c:3613:1: warning: type of 'show_code' defaults to 'int' [-Wimplicit-int] init_update_data(show_code) { ^~~~~~~~~~~~~~~~ --- init_fs.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- init_fy.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTY initfa.c -o init_fy.o --- init_fx.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- init_tfx.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- init_tfy.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTY -DTFAST initfa.c -o init_tfy.o --- drop_tfz.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST dropfz3.c -o drop_tfz.o dropfz3.c: In function 'init_update_data': dropfz3.c:3587:1: warning: type of 'show_code' defaults to 'int' [-Wimplicit-int] init_update_data(show_code) { ^~~~~~~~~~~~~~~~ --- init_fy.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- init_tfs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS -DTFAST initfa.c -o init_tfs.o --- drop_tfs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o --- init_tfy.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- calcons_tfs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTS -c cal_consf.c -o calcons_tfs.o --- init_fm.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM initfa.c -o init_fm.o --- tatstats_fm.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM tatstats.c -o tatstats_fm.o --- drop_fm.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM dropfs2.c -o drop_fm.o --- init_tfs.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- calcons_fm.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTM -c cal_consf.c -o calcons_fm.o --- mshowalign2_s.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mshowalign2.c -o mshowalign2_s.o --- init_tfm.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTM -DTFAST initfa.c -o init_tfm.o --- drop_tfm.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o --- mshowalign2_s.o --- In file included from mshowalign2.c:33: mshowalign2.c: In function 'showalign': defs.h:25:41: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] #define SAFE_STRNCPY(dest,src,dest_len) strncpy(dest,src,dest_len); dest[dest_len-1]='\0' ^~~~~~~~~~~~~~~~~~~~~~~~~~ mshowalign2.c:561:8: note: in expansion of macro 'SAFE_STRNCPY' SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); ^~~~~~~~~~~~ --- calcons_tfm.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTM -c cal_consf.c -o calcons_tfm.o --- init_fm.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- init_ff.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF initfa.c -o init_ff.o --- init_tfm.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- scaleswtf.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTF -c scaleswt.c -o scaleswtf.o --- tatstats_ff.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF tatstats.c -o tatstats_ff.o --- calcons_ff.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTF -c cal_consf.c -o calcons_ff.o --- init_tf.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF -DTFAST initfa.c -o init_tf.o --- drop_tff.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF -DTFAST dropff2.c -o drop_tff.o --- init_ff.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- calcons_tff.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DTFAST -DFASTF -c cal_consf.c -o calcons_tff.o --- scale_sn.o --- cc -DNORMAL_DIST -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c scaleswn.c -o scale_sn.o --- init_lnw.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DGLSEARCH initfa.c -o init_lnw.o --- gwm_align.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DGGSEARCH -c wm_align.c -o gwm_align.o --- init_gnw.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DGGSEARCH initfa.c -o init_gnw.o --- dropgnw.o --- cc -DGLOBAL_GLOBAL -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnnw2.c -o dropgnw.o --- comp_mthr9.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -DCOMP_MLIB -c comp_lib9.c -o comp_mthr9.o --- init_tf.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- work_thr2.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c work_thr2.c --- pthr_subs2.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c pthr_subs2.c --- init_gnw.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- init_lnw.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- compacc2_t.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -DCOMP_MLIB -c compacc2e.c -o compacc2_t.o --- showbest.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mshowbest.c -o showbest.o --- build_ares.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c build_ares.c -o build_ares.o --- re_getlib.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c re_getlib.c --- build_ares.o --- build_ares.c: In function 'build_ares_code': build_ares.c:178:2: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(cur_ares_p->annot_var_s,annot_var_dyn->string,strlen(annot_var_dyn->string)+2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build_ares.c:178:56: note: length computed here strncpy(cur_ares_p->annot_var_s,annot_var_dyn->string,strlen(annot_var_dyn->string)+2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- mshowalign2_t.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DCOMP_THR -c mshowalign2.c -o mshowalign2_t.o --- htime.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c htime.c --- apam.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c apam.c --- mshowalign2_t.o --- In file included from mshowalign2.c:33: mshowalign2.c: In function 'showalign': defs.h:25:41: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] #define SAFE_STRNCPY(dest,src,dest_len) strncpy(dest,src,dest_len); dest[dest_len-1]='\0' ^~~~~~~~~~~~~~~~~~~~~~~~~~ mshowalign2.c:561:8: note: in expansion of macro 'SAFE_STRNCPY' SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); ^~~~~~~~~~~~ --- doinit.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c doinit.c --- init_fa.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTA initfa.c -o init_fa.o --- doinit.o --- doinit.c: In function 'add_annot_def': doinit.c:607:7: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'pre_parse_markx', inlined from 'initenv' at doinit.c:384:4: doinit.c:759:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ doinit.c: In function 'set_opt_disp_defs': doinit.c:953:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(this_opt->s_param,s_param,strlen(s_param)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- scale_se.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DLOCAL_SCORE -c scaleswn.c -o scale_se.o --- karlin.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c karlin.c --- init_fa.o --- initfa.c: In function 'get_lambda': initfa.c:2194:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from initfa.c:43: /usr/include/stdlib.h:93:7: note: in a call to allocation function 'calloc' declared here void *calloc(size_t, size_t) __alloc_size2(1, 2) __malloclike __heedresult; ^~~~~~ --- compacc2_t.o --- compacc2e.c: In function 'next_annot_entry': compacc2e.c:1990:2: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- drop_nfa.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnfa.c -o drop_nfa.o --- wm_align.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c wm_align.c --- calcons_fa.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTA -c cal_cons2.c -o calcons_fa.o cal_cons2.c: In function 'init_update_data': cal_cons2.c:894:1: warning: type of 'show_code' defaults to 'int' [-Wimplicit-int] init_update_data(show_code) { ^~~~~~~~~~~~~~~~ --- lgetlib.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c nmgetlib.c -o lgetlib.o nmgetlib.c: In function 'vranlib': nmgetlib.c:1494:5: warning: 'strncat' specified bound 1 equals source length [-Wstringop-overflow=] strncat(str," ",(size_t)1); ^~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'gcg_getlib': nmgetlib.c:1556:7: warning: 'strncat' specified bound 1 equals source length [-Wstringop-overflow=] strncat(libstr," ",1); ^~~~~~~~~~~~~~~~~~~~~ nmgetlib.c: In function 'gcg_ranlib': nmgetlib.c:1640:5: warning: 'strncat' specified bound 1 equals source length [-Wstringop-overflow=] strncat(str," ",(size_t)1); ^~~~~~~~~~~~~~~~~~~~~~~~~~ --- lgetaa_m.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mmgetaa.c -o lgetaa_m.o --- c_dispn.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c c_dispn.c --- ncbl2_mlib.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c ncbl2_mlib.c -o ncbl2_mlib.o --- lib_sel.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c lib_sel.c lib_sel.c: In function 'add_file': lib_sel.c:316:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(lbptr,tname,len); ^~~~~~~~~~~~~~~~~~~~~~~~ lib_sel.c:310:7: note: length computed here len=strlen(tname)+1; ^~~~~~~~~~~~~ --- url_subs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c url_subs.c --- mrandom.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c mrandom.c --- dropgsw2.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropgsw2.c -o dropgsw2.o --- url_subs.o --- In file included from url_subs.c:25: url_subs.c: In function 'encode_json_lines': defs.h:25:41: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] #define SAFE_STRNCPY(dest,src,dest_len) strncpy(dest,src,dest_len); dest[dest_len-1]='\0' ^~~~~~~~~~~~~~~~~~~~~~~~~~ url_subs.c:72:3: note: in expansion of macro 'SAFE_STRNCPY' SAFE_STRNCPY(tmp_annot_s, annot_s, n_tmp_annot_s); ^~~~~~~~~~~~ url_subs.c:65:19: note: length computed here n_tmp_annot_s = strlen(annot_s)+1; ^~~~~~~~~~~~~~~ --- pssm_asn_subs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c pssm_asn_subs.c --- last_thresh.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c last_thresh.c --- lsim4.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c lsim4.c --- scaleswts.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c scaleswt.c -o scaleswts.o --- last_tat.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c last_tat.c --- tatstats_fs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTS tatstats.c -o tatstats_fs.o --- lgetlib.o --- nmgetlib.c: In function 'alloc_file_name': nmgetlib.c:2251:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(alloc_f_name,f_name,fn_len); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nmgetlib.c:2244:12: note: length computed here fn_len = strlen(f_name); ^~~~~~~~~~~~~~ --- drop_fs2.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTS -c dropfs2.c -o drop_fs2.o --- calcons_fs.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -DFASTS -c cal_consf.c -o calcons_fs.o --- faatran.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c faatran.c --- drop_fx.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropfx2.c -o drop_fx.o dropfx2.c: In function 'init_update_data': dropfx2.c:3613:1: warning: type of 'show_code' defaults to 'int' [-Wimplicit-int] init_update_data(show_code) { ^~~~~~~~~~~~~~~~ --- drop_fz.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropfz3.c -o drop_fz.o --- drop_ff2.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c -DFASTF dropff2.c -o drop_ff2.o --- drop_fz.o --- dropfz3.c: In function 'init_update_data': dropfz3.c:3587:1: warning: type of 'show_code' defaults to 'int' [-Wimplicit-int] init_update_data(show_code) { ^~~~~~~~~~~~~~~~ --- droplnw.o --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -c dropnnw2.c -o droplnw.o --- map_db --- cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -o ../bin/map_db map_db.c map_db.c: In function 'newname': map_db.c:568:3: warning: 'strncat' specified bound 1 equals source length [-Wstringop-overflow=] strncat(nname,".",1); ^~~~~~~~~~~~~~~~~~~~ --- fasta36 --- cc -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- ssearch36 --- cc -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw.o dropgsw2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread --- ggsearch36 --- cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw.o dropgnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- fastm36 --- cc -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread --- ssearch36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- tfastf36 --- cc -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread --- fastm36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- tfasts36 --- cc -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread --- tfastf36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- tfastm36 --- cc -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread --- tfasts36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- tfastx36 --- cc -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread --- tfastm36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- tfasty36 --- cc -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread --- tfastx36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- fasts36 --- cc -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread --- tfasty36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- lalign36 --- cc -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz --- glsearch36 --- cc -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw.o droplnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread --- fasts36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- fastf36 --- cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread --- lalign36 --- compacc2_s.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- glsearch36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- fastf36 --- compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- fasty36 --- cc -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() --- fastx36 --- cc -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for fasta3-36.3.8 ===> Generating temporary packing list cc -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw.o dropgsw2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz compacc2_s.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/fastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fx.o drop_fx.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/tfasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfy.o drop_tfz.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw.o droplnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw.o dropgnw.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lz -pthread compacc2_t.o:compacc2e.c:function build_lib_db: warning: warning: mktemp() possibly used unsafely; consider using mkstemp() cc -pipe -O2 -fno-strict-aliasing -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DHAS_INTTYPES -DSAMP_STATS -DSFCHAR="':'" -DFASTA_HOST='pkgbox64.dragonflybsd.org' -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC -o ../bin/map_db map_db.c map_db.c: In function 'newname': map_db.c:568:3: warning: 'strncat' specified bound 1 equals source length [-Wstringop-overflow=] strncat(nname,".",1); ^~~~~~~~~~~~~~~~~~~~ cd ../bin; cp fasta36 ssearch36 lalign36 fasts36 fastx36 tfastx36 fasty36 tfasty36 tfasts36 fastm36 tfastm36 fastf36 tfastf36 glsearch36 ggsearch36 map_db /construction/biology/fasta3/stage/usr/local/bin; cd ../src (cd /construction/biology/fasta3/fasta-36.3.8/bin && install -s -m 555 * /construction/biology/fasta3/stage/usr/local/bin) (cd /construction/biology/fasta3/fasta-36.3.8/conf && install -m 0644 fastlibs /construction/biology/fasta3/stage/usr/local/etc/fastlibs.sample) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 data/*.mat /construction/biology/fasta3/stage/usr/local/share/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 444 fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 444 fastf3.1 /construction/biology/fasta3/stage/usr/local/man/man1) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 444 fasts3.1 /construction/biology/fasta3/stage/usr/local/man/man1) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 444 prss3.1 /construction/biology/fasta3/stage/usr/local/man/man1) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 444 map_db.1 /construction/biology/fasta3/stage/usr/local/man/man1) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 444 ps_lav.1 /construction/biology/fasta3/stage/usr/local/man/man1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/fastf35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/fasts35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/fastm35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/fastx35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/fasty35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/ggsearch35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/lalign35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/ssearch35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/tfasta35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/tfastf35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/tfasts35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/tfastx35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/tfasty35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/prfx35.1) (ln -sf fasta36.1 /construction/biology/fasta3/stage/usr/local/man/man1/prss35.1) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 COPYRIGHT /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 FASTA_LIST /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 README /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 0644 README.versions /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 0644 fasta_func.doc /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 0644 readme.* /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 0644 fasta.defaults /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 0644 fasta.options /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 0644 fasta_versions.html /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8/doc && install -m 0644 changes*.html /construction/biology/fasta3/stage/usr/local/share/doc/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 seq/*.aa /construction/biology/fasta3/stage/usr/local/share/examples/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 seq/*.lc /construction/biology/fasta3/stage/usr/local/share/examples/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 seq/*.seq /construction/biology/fasta3/stage/usr/local/share/examples/fasta3) (cd /construction/biology/fasta3/fasta-36.3.8 && install -m 0644 seq/*.lib /construction/biology/fasta3/stage/usr/local/share/examples/fasta3) ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for fasta3-36.3.8 file sizes/checksums [128]: .. done packing files [128]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:14:37 UTC Duration: 00:00:31