-------------------------------------------------------------------------------
-- Phase: Environment
-------------------------------------------------------------------------------

NO_DEPENDS=1
UNAME_r=6.1
UNAME_m=x86_64
UNAME_p=x86_64
UNAME_v=unknown
UNAME_s=DragonFly
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin
SSL_NO_VERIFY_PEER=1
LANG=C
HOME=/root
USER=root
TERM=dumb

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: showconfig
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: CONFIGURE_ENV
-------------------------------------------------------------------------------

MAKE=gmake PYTHON="/usr/local/bin/python3.8" XDG_DATA_HOME=/construction/biology/stacks  XDG_CONFIG_HOME=/construction/biology/stacks  HOME=/construction/biology/stacks TMPDIR="/tmp" PATH=/construction/biology/stacks/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: CONFIGURE_ARGS
-------------------------------------------------------------------------------

--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: MAKE_ENV
-------------------------------------------------------------------------------

XDG_DATA_HOME=/construction/biology/stacks  XDG_CONFIG_HOME=/construction/biology/stacks  HOME=/construction/biology/stacks TMPDIR="/tmp" PATH=/construction/biology/stacks/.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=" -lpthread " 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"

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: MAKE_ARGS
-------------------------------------------------------------------------------

DESTDIR=/construction/biology/stacks/stage

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: PLIST_SUB
-------------------------------------------------------------------------------

PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/stacks"  EXAMPLESDIR="share/examples/stacks"  DATADIR="share/stacks"  WWWDIR="www/stacks"  ETCDIR="etc/stacks"

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: SUB_LIST
-------------------------------------------------------------------------------

PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/stacks DOCSDIR=/usr/local/share/doc/stacks EXAMPLESDIR=/usr/local/share/examples/stacks  WWWDIR=/usr/local/www/stacks ETCDIR=/usr/local/etc/stacks

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: /etc/make.conf
-------------------------------------------------------------------------------

DPORTS_BUILDER=yes
DISABLE_LICENSES=yes
DEFAULT_VERSIONS=ssl=openssl
FORCE_PACKAGE=yes
DEVELOPER=yes
USE_PACKAGE_DEPENDS_ONLY=yes
PORTSDIR=/xports
PORT_DBDIR=/options
PKG_DBDIR=/var/db/pkg
PKG_CACHEDIR=/var/cache/pkg
PKG_SUFX=.txz
DEVELOPER=1
UID=0
ARCH=x86_64
OPSYS=DragonFly
DFLYVERSION=600102
OSVERSION=9999999
OSREL=6.1
_OSRELEASE=6.1-SYNTH
DISTDIR=/distfiles
WRKDIRPREFIX=/construction
BATCH=yes
PACKAGE_BUILDING=yes
PKG_CREATE_VERBOSE=yes
MAKE_JOBS_NUMBER=10

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: setup
-------------------------------------------------------------------------------

Installing /packages/All/indexinfo-0.3.1.txz
Installing /packages/All/gettext-runtime-0.21.txz
Installing /packages/All/gmake-4.3_2.txz
Installing /packages/All/libffi-3.3_1.txz
Installing /packages/All/expat-2.4.1.txz
Installing /packages/All/mpdecimal-2.5.1.txz
Installing /packages/All/ncurses-6.2.20210626.txz
=====
Message from ncurses-6.2.20210626:

--
{
	type: install
	message: <<EOM
To get the terminfo database please install the terminfo-db package:
pkg install terminfo-db
EOL
}
Installing /packages/All/readline-8.1.1.txz
Installing /packages/All/openssl-1.1.1l,1.txz
Installing /packages/All/python38-3.8.10.txz
=====
Message from python38-3.8.10:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py38-gdbm       databases/py-gdbm@py38
py38-sqlite3    databases/py-sqlite3@py38
py38-tkinter    x11-toolkits/py-tkinter@py38

SUCCEEDED 00:00:08

-------------------------------------------------------------------------------
-- Phase: check-sanity
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: pkg-depends
-------------------------------------------------------------------------------

===>   stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found

SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: fetch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: fetch
-------------------------------------------------------------------------------

===>   stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by stacks-2.4_2 for building

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: checksum
-------------------------------------------------------------------------------

===>   stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by stacks-2.4_2 for building
=> SHA256 Checksum OK for stacks-2.4.tar.gz.

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract
-------------------------------------------------------------------------------

===>   stacks-2.4_2 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by stacks-2.4_2 for building
===>  Extracting for stacks-2.4_2
=> SHA256 Checksum OK for stacks-2.4.tar.gz.

Extracted Memory Use:  54.80M
SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: patch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: patch
-------------------------------------------------------------------------------

===>  Patching for stacks-2.4_2

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: build-depends
-------------------------------------------------------------------------------

===>   stacks-2.4_2 depends on package: gmake>=4.3 - found
===>   stacks-2.4_2 depends on file: /usr/local/bin/python3.8 - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: lib-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: configure
-------------------------------------------------------------------------------

===>   stacks-2.4_2 depends on package: gmake>=4.3 - found
===>   stacks-2.4_2 depends on file: /usr/local/bin/python3.8 - found
===>  Configuring for stacks-2.4_2
configure: loading site script /xports/Templates/config.site
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking whether gmake supports nested variables... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking for style of include used by gmake... GNU
checking dependency style of c++... gcc3
checking for gcc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking whether cc understands -c and -o together... yes
checking whether c++ supports C++11 features by default... yes
checking for ranlib... ranlib
checking for ar... ar
checking the archiver (ar) interface... ar
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for float.h... (cached) yes
checking for limits.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for cc option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... (cached) yes
checking for _Bool... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... (cached) yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... (cached) yes
checking for pow... no
checking for sqrt... no
checking for clock_gettime... (cached) yes
checking for functional regular expressions... yes
checking for gawk... (cached) /usr/bin/awk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating htslib/Makefile
config.status: creating config.h
config.status: executing depfiles commands

SUCCEEDED 00:00:14

-------------------------------------------------------------------------------
-- Phase: build
-------------------------------------------------------------------------------

===>  Building for stacks-2.4_2
gmake[1]: Entering directory '/construction/biology/stacks/stacks-2.4'
gmake  all-recursive
gmake[2]: Entering directory '/construction/biology/stacks/stacks-2.4'
Making all in htslib
gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4/htslib'
depbase=`echo bcf_sr_sort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT bcf_sr_sort.o -MD -MP -MF $depbase.Tpo -c -o bcf_sr_sort.o bcf_sr_sort.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo bgzf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT bgzf.o -MD -MP -MF $depbase.Tpo -c -o bgzf.o bgzf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo bgzip.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT bgzip.o -MD -MP -MF $depbase.Tpo -c -o bgzip.o bgzip.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo errmod.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT errmod.o -MD -MP -MF $depbase.Tpo -c -o errmod.o errmod.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo faidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT faidx.o -MD -MP -MF $depbase.Tpo -c -o faidx.o faidx.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo hfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT hfile.o -MD -MP -MF $depbase.Tpo -c -o hfile.o hfile.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo hfile_net.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT hfile_net.o -MD -MP -MF $depbase.Tpo -c -o hfile_net.o hfile_net.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo hts.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT hts.o -MD -MP -MF $depbase.Tpo -c -o hts.o hts.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo hts_os.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT hts_os.o -MD -MP -MF $depbase.Tpo -c -o hts_os.o hts_os.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo htsfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT htsfile.o -MD -MP -MF $depbase.Tpo -c -o htsfile.o htsfile.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo kfunc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT kfunc.o -MD -MP -MF $depbase.Tpo -c -o kfunc.o kfunc.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo knetfile.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT knetfile.o -MD -MP -MF $depbase.Tpo -c -o knetfile.o knetfile.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo kstring.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT kstring.o -MD -MP -MF $depbase.Tpo -c -o kstring.o kstring.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo multipart.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT multipart.o -MD -MP -MF $depbase.Tpo -c -o multipart.o multipart.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo probaln.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT probaln.o -MD -MP -MF $depbase.Tpo -c -o probaln.o probaln.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo realn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT realn.o -MD -MP -MF $depbase.Tpo -c -o realn.o realn.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo regidx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT regidx.o -MD -MP -MF $depbase.Tpo -c -o regidx.o regidx.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo sam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT sam.o -MD -MP -MF $depbase.Tpo -c -o sam.o sam.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo synced_bcf_reader.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT synced_bcf_reader.o -MD -MP -MF $depbase.Tpo -c -o synced_bcf_reader.o synced_bcf_reader.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo tabix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT tabix.o -MD -MP -MF $depbase.Tpo -c -o tabix.o tabix.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo tbx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT tbx.o -MD -MP -MF $depbase.Tpo -c -o tbx.o tbx.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo textutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT textutils.o -MD -MP -MF $depbase.Tpo -c -o textutils.o textutils.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo thread_pool.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT thread_pool.o -MD -MP -MF $depbase.Tpo -c -o thread_pool.o thread_pool.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT vcf.o -MD -MP -MF $depbase.Tpo -c -o vcf.o vcf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcf_sweep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT vcf_sweep.o -MD -MP -MF $depbase.Tpo -c -o vcf_sweep.o vcf_sweep.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo vcfutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT vcfutils.o -MD -MP -MF $depbase.Tpo -c -o vcfutils.o vcfutils.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_codecs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_codecs.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_codecs.o cram/cram_codecs.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_decode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_decode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_decode.o cram/cram_decode.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_encode.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_encode.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_encode.o cram/cram_encode.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_external.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_external.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_external.o cram/cram_external.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_index.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_index.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_index.o cram/cram_index.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_io.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_io.o cram/cram_io.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_samtools.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_samtools.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_samtools.o cram/cram_samtools.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/cram_stats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/cram_stats.o -MD -MP -MF $depbase.Tpo -c -o cram/cram_stats.o cram/cram_stats.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/files.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/files.o -MD -MP -MF $depbase.Tpo -c -o cram/files.o cram/files.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/mFILE.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/mFILE.o -MD -MP -MF $depbase.Tpo -c -o cram/mFILE.o cram/mFILE.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/open_trace_file.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/open_trace_file.o -MD -MP -MF $depbase.Tpo -c -o cram/open_trace_file.o cram/open_trace_file.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/pooled_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/pooled_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/pooled_alloc.o cram/pooled_alloc.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/rANS_static.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/rANS_static.o -MD -MP -MF $depbase.Tpo -c -o cram/rANS_static.o cram/rANS_static.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/sam_header.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/sam_header.o -MD -MP -MF $depbase.Tpo -c -o cram/sam_header.o cram/sam_header.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cram/string_alloc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT cram/string_alloc.o -MD -MP -MF $depbase.Tpo -c -o cram/string_alloc.o cram/string_alloc.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo os/rand.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I..     -pipe -O2 -fno-strict-aliasing  -MT os/rand.o -MD -MP -MF $depbase.Tpo -c -o os/rand.o os/rand.c &&\
mv -f $depbase.Tpo $depbase.Po
rm -f libhts.a
ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o 
/usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libhts.a
gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4/htslib'
gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4'
depbase=`echo src/aln_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/aln_utils.o -MD -MP -MF $depbase.Tpo -c -o src/aln_utils.o src/aln_utils.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/BamI.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/BamI.o -MD -MP -MF $depbase.Tpo -c -o src/BamI.o src/BamI.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/catalog_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/catalog_utils.o -MD -MP -MF $depbase.Tpo -c -o src/catalog_utils.o src/catalog_utils.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/cmb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/cmb.o -MD -MP -MF $depbase.Tpo -c -o src/cmb.o src/cmb.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/constants.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/constants.o -MD -MP -MF $depbase.Tpo -c -o src/constants.o src/constants.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/DNANSeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/DNANSeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNANSeq.o src/DNANSeq.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/DNASeq4.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/DNASeq4.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq4.o src/DNASeq4.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/DNASeq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/DNASeq.o -MD -MP -MF $depbase.Tpo -c -o src/DNASeq.o src/DNASeq.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/gzFasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/gzFasta.o -MD -MP -MF $depbase.Tpo -c -o src/gzFasta.o src/gzFasta.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/input.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/input.o -MD -MP -MF $depbase.Tpo -c -o src/input.o src/input.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/kmers.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/kmers.o -MD -MP -MF $depbase.Tpo -c -o src/kmers.o src/kmers.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/locus.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/locus.o -MD -MP -MF $depbase.Tpo -c -o src/locus.o src/locus.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/log_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/log_utils.o -MD -MP -MF $depbase.Tpo -c -o src/log_utils.o src/log_utils.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/MetaPopInfo.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/MetaPopInfo.o -MD -MP -MF $depbase.Tpo -c -o src/MetaPopInfo.o src/MetaPopInfo.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/models.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/models.o -MD -MP -MF $depbase.Tpo -c -o src/models.o src/models.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mstack.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/mstack.o -MD -MP -MF $depbase.Tpo -c -o src/mstack.o src/mstack.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/mst.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/mst.o -MD -MP -MF $depbase.Tpo -c -o src/mst.o src/mst.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/nucleotides.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/nucleotides.o -MD -MP -MF $depbase.Tpo -c -o src/nucleotides.o src/nucleotides.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/renz.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/renz.o -MD -MP -MF $depbase.Tpo -c -o src/renz.o src/renz.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/Seq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/Seq.o -MD -MP -MF $depbase.Tpo -c -o src/Seq.o src/Seq.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/sql_utilities.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/sql_utilities.o -MD -MP -MF $depbase.Tpo -c -o src/sql_utilities.o src/sql_utilities.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/stacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/stacks.o -MD -MP -MF $depbase.Tpo -c -o src/stacks.o src/stacks.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/utils.o -MD -MP -MF $depbase.Tpo -c -o src/utils.o src/utils.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/Vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/Vcf.o -MD -MP -MF $depbase.Tpo -c -o src/Vcf.o src/Vcf.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/clean.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/clean.o -MD -MP -MF $depbase.Tpo -c -o src/clean.o src/clean.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/file_io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/file_io.o -MD -MP -MF $depbase.Tpo -c -o src/file_io.o src/file_io.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/write.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/write.o -MD -MP -MF $depbase.Tpo -c -o src/write.o src/write.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/export_formats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/export_formats.o -MD -MP -MF $depbase.Tpo -c -o src/export_formats.o src/export_formats.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/genotype_dictionaries.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/genotype_dictionaries.o -MD -MP -MF $depbase.Tpo -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/PopSum.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/PopSum.o -MD -MP -MF $depbase.Tpo -c -o src/PopSum.o src/PopSum.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/Hwp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/Hwp.o -MD -MP -MF $depbase.Tpo -c -o src/Hwp.o src/Hwp.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/ustacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/ustacks.o -MD -MP -MF $depbase.Tpo -c -o src/ustacks.o src/ustacks.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/cstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/cstacks.o -MD -MP -MF $depbase.Tpo -c -o src/cstacks.o src/cstacks.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/sstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/sstacks.o -MD -MP -MF $depbase.Tpo -c -o src/sstacks.o src/sstacks.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/process_radtags.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/process_radtags.o -MD -MP -MF $depbase.Tpo -c -o src/process_radtags.o src/process_radtags.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/process_shortreads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/process_shortreads.o -MD -MP -MF $depbase.Tpo -c -o src/process_shortreads.o src/process_shortreads.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/kmer_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/kmer_filter.o -MD -MP -MF $depbase.Tpo -c -o src/kmer_filter.o src/kmer_filter.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/clone_filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/clone_filter.o -MD -MP -MF $depbase.Tpo -c -o src/clone_filter.o src/clone_filter.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/populations.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/populations.o -MD -MP -MF $depbase.Tpo -c -o src/populations.o src/populations.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/phasedstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/phasedstacks.o -MD -MP -MF $depbase.Tpo -c -o src/phasedstacks.o src/phasedstacks.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/tsv2bam.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/tsv2bam.o -MD -MP -MF $depbase.Tpo -c -o src/tsv2bam.o src/tsv2bam.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/gstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/gstacks.o -MD -MP -MF $depbase.Tpo -c -o src/gstacks.o src/gstacks.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/debruijn.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/debruijn.o -MD -MP -MF $depbase.Tpo -c -o src/debruijn.o src/debruijn.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/SuffixTree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I.  -fopenmp -I./htslib   -pipe -O2 -fno-strict-aliasing  -MT src/SuffixTree.o -MD -MP -MF $depbase.Tpo -c -o src/SuffixTree.o src/SuffixTree.cc &&\
mv -f $depbase.Tpo $depbase.Po
rm -f libcore.a
ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o  
/usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcore.a
rm -f libclean.a
ar cru libclean.a src/clean.o src/file_io.o src/write.o 
/usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libclean.a
rm -f libpop.a
ar cru libpop.a src/export_formats.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o 
/usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libpop.a
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o cstacks src/cstacks.o htslib/libhts.a libcore.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o process_radtags src/process_radtags.o htslib/libhts.a libcore.a libclean.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o process_shortreads src/process_shortreads.o htslib/libhts.a libcore.a libclean.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o kmer_filter src/kmer_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o ustacks src/ustacks.o htslib/libhts.a libcore.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o clone_filter src/clone_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o sstacks src/sstacks.o htslib/libhts.a libcore.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o phasedstacks src/phasedstacks.o htslib/libhts.a libcore.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o populations src/populations.o htslib/libhts.a libcore.a libpop.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o tsv2bam src/tsv2bam.o htslib/libhts.a libcore.a -lz -lgomp 
c++  -pipe -O2 -fno-strict-aliasing  -fopenmp -lpthread  -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o htslib/libhts.a libcore.a -lz -lgomp 
gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4'
gmake[2]: Leaving directory '/construction/biology/stacks/stacks-2.4'
gmake[1]: Leaving directory '/construction/biology/stacks/stacks-2.4'

SUCCEEDED 00:02:05

-------------------------------------------------------------------------------
-- Phase: run-depends
-------------------------------------------------------------------------------

===>   stacks-2.4_2 depends on file: /usr/local/bin/python3.8 - found

SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: stage
-------------------------------------------------------------------------------

===>  Staging for stacks-2.4_2
===>   stacks-2.4_2 depends on file: /usr/local/bin/python3.8 - found
===>   Generating temporary packing list
gmake[1]: Entering directory '/construction/biology/stacks/stacks-2.4'
Making install in htslib
gmake[2]: Entering directory '/construction/biology/stacks/stacks-2.4/htslib'
gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4/htslib'
gmake[3]: Nothing to be done for 'install-exec-am'.
gmake[3]: Nothing to be done for 'install-data-am'.
gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4/htslib'
gmake[2]: Leaving directory '/construction/biology/stacks/stacks-2.4/htslib'
gmake[2]: Entering directory '/construction/biology/stacks/stacks-2.4'
gmake[3]: Entering directory '/construction/biology/stacks/stacks-2.4'
 /bin/mkdir -p '/construction/biology/stacks/stage/usr/local/bin'
  install  -s -m 555 ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/construction/biology/stacks/stage/usr/local/bin'
 /bin/mkdir -p '/construction/biology/stacks/stage/usr/local/bin'
 install  -m 555 scripts/denovo_map.pl scripts/ref_map.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb '/construction/biology/stacks/stage/usr/local/bin'
gmake  install-data-hook
gmake[4]: Entering directory '/construction/biology/stacks/stacks-2.4'
sed -e 's,_VERSION_,2.4,' -e 's,_BINDIR_,/usr/local/bin/,g' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl > /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl.subst
mv /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl.subst /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl
chmod +x /construction/biology/stacks/stage/usr/local/bin/denovo_map.pl
sed -e 's,_VERSION_,2.4,' -e 's,_BINDIR_,/usr/local/bin/,g' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /construction/biology/stacks/stage/usr/local/bin/ref_map.pl > /construction/biology/stacks/stage/usr/local/bin/ref_map.pl.subst
mv /construction/biology/stacks/stage/usr/local/bin/ref_map.pl.subst /construction/biology/stacks/stage/usr/local/bin/ref_map.pl
chmod +x /construction/biology/stacks/stage/usr/local/bin/ref_map.pl
sed -i.bkp -e 's,_VERSION_,2.4,' /construction/biology/stacks/stage/usr/local/bin/stacks-integrate-alignments
rm -f /construction/biology/stacks/stage/usr/local/bin/stacks-integrate-alignments.bkp
chmod +x /construction/biology/stacks/stage/usr/local/bin/stacks-integrate-alignments
chmod +x /construction/biology/stacks/stage/usr/local/bin/stacks-dist-extract
chmod +x /construction/biology/stacks/stage/usr/local/bin/stacks-gdb
gmake[4]: Leaving directory '/construction/biology/stacks/stacks-2.4'
gmake[3]: Leaving directory '/construction/biology/stacks/stacks-2.4'
gmake[2]: Leaving directory '/construction/biology/stacks/stacks-2.4'
gmake[1]: Leaving directory '/construction/biology/stacks/stacks-2.4'
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks

SUCCEEDED 00:00:02

-------------------------------------------------------------------------------
-- Phase: check-plist
-------------------------------------------------------------------------------

====> Checking for pkg-plist issues (check-plist)
===> Parsing plist
===> Checking for items in STAGEDIR missing from pkg-plist
===> Checking for items in pkg-plist which are not in STAGEDIR
===> No pkg-plist issues found (check-plist)

SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: package
-------------------------------------------------------------------------------

===>  Building package for stacks-2.4_2
file sizes/checksums    [18]:   0%
file sizes/checksums    [18]: 100%
packing files           [18]:   0%
packing files           [18]: 100%
packing directories      [0]:   0%
packing directories      [0]: 100%

SUCCEEDED 00:00:07
TOTAL TIME 00:02:42