=>> Building biology/stacks build started at Tue Jan 20 16:28:40 EST 2026 port directory: /usr/ports/biology/stacks package name: stacks-2.68 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 558 Jan 23 2025 /usr/ports/biology/stacks/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: 989b3863994b Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 02 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p7 1403000 UNAME_r=14.3-RELEASE-p7 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/02/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stacks/work/.cache HOME=/wrkdirs/usr/ports/biology/stacks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stacks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stacks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stacks/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/stacks/work/.cache HOME=/wrkdirs/usr/ports/biology/stacks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stacks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/stacks/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -lpthread " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/stacks" EXAMPLESDIR="share/examples/stacks" DATADIR="share/stacks" WWWDIR="www/stacks" ETCDIR="etc/stacks" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" 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 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> stacks-2.68 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> stacks-2.68 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of stacks-2.68 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by stacks-2.68 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by stacks-2.68 for building => SHA256 Checksum OK for stacks-2.68.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by stacks-2.68 for building ===> Extracting for stacks-2.68 => SHA256 Checksum OK for stacks-2.68.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for stacks-2.68 ===> Applying FreeBSD patches for stacks-2.68 from /usr/ports/biology/stacks/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> stacks-2.68 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> stacks-2.68 depends on package: gmake>=4.4.1 - found ===> Returning to build of stacks-2.68 ===> stacks-2.68 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.14.pkg [pkg.DaveG.ca] Installing python311-3.11.14... [pkg.DaveG.ca] `-- Installing libffi-3.5.1... [pkg.DaveG.ca] `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] `-- Installing readline-8.3.3... [pkg.DaveG.ca] `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] Extracting python311-3.11.14: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> stacks-2.68 depends on file: /usr/local/bin/python3.11 - found ===> Returning to build of stacks-2.68 ===> stacks-2.68 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> stacks-2.68 depends on file: /usr/local/bin/ccache - found ===> Returning to build of stacks-2.68 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for stacks-2.68 configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/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 the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 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 for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep 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 _Bool... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking whether closedir returns void... no checking build system type... amd64-portbld-freebsd14.3 checking host system type... amd64-portbld-freebsd14.3 checking for GNU libc compatible malloc... (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 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for stacks-2.68 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' Making all in htslib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68/htslib' depbase=`echo bcf_sr_sort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcf_sweep.o -MD -MP -MF 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cram/sam_header.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -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.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT os/rand.o -MD -MP -MF $depbase.Tpo -c -o os/rand.o os/rand.c &&\ mv -f $depbase.Tpo $depbase.Po rm -f libhts.a ar cru libhts.a bcf_sr_sort.o bgzf.o bgzip.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o htsfile.o kfunc.o knetfile.o kstring.o md5.o multipart.o os/rand.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o tabix.o tbx.o textutils.o thread_pool.o vcf.o vcf_sweep.o vcfutils.o ranlib libhts.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68/htslib' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' depbase=`echo src/ustacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/ustacks.o -MD -MP -MF $depbase.Tpo -c -o src/ustacks.o src/ustacks.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/aln_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong 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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 -O2 -pipe -fstack-protector-strong -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 $depbase.Po depbase=`echo src/clean.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/write.o -MD -MP -MF $depbase.Tpo -c -o src/write.o src/write.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/process_shortreads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/populations.o -MD -MP -MF $depbase.Tpo -c -o src/populations.o src/populations.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/bootstrap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/bootstrap.o -MD -MP -MF $depbase.Tpo -c -o src/bootstrap.o src/bootstrap.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 -O2 -pipe -fstack-protector-strong -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 $depbase.Po depbase=`echo src/mapping_utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/mapping_utils.o -MD -MP -MF $depbase.Tpo -c -o src/mapping_utils.o src/mapping_utils.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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/Hwp.o -MD -MP -MF $depbase.Tpo -c -o src/Hwp.o src/Hwp.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/phasedstacks.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 -O2 -pipe -fstack-protector-strong -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 In file included from src/DNASeq4.cc:1: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: src/DNASeq4.cc:96:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | *this = move(seq); | ^ | std:: 3 warnings generated. In file included from src/gzFasta.cc:21: In file included from src/gzFasta.h:24: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/gzFasta.cc:21: In file included from src/gzFasta.h:24: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 4 warnings generated. In file included from src/input.cc:25: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/input.cc:25: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 4 warnings generated. In file included from src/BamI.cc:6: In file included from src/BamI.h:36: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/BamI.cc:6: In file included from src/BamI.h:36: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/BamI.cc:157:9: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 157 | hdr(move(header)), | ^ | std:: 5 warnings generated. In file included from src/clean.cc:25: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/clean.cc:25: In file included from src/clean.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/clean.cc:25: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/clean.cc:25: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/clean.cc:25: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. In file included from src/stacks.cc:33: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/stacks.cc:33: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 4 warnings generated. In file included from src/sql_utilities.cc:1: In file included from src/sql_utilities.h:29: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/sql_utilities.cc:1: In file included from src/sql_utilities.h:29: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 4 warnings generated. In file included from src/kmers.cc:24: In file included from src/kmers.h:35: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/kmers.cc:24: In file included from src/kmers.h:35: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/kmers.cc:24: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/kmers.cc:24: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/kmers.cc:24: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. In file included from src/write.cc:29: In file included from src/write.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:31: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:31: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/write.cc:29: In file included from src/write.h:31: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. In file included from src/SuffixTree.cc:21: In file included from src/SuffixTree.h:29: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: 2 warnings generated. In file included from src/bootstrap.cc:21: In file included from src/bootstrap.h:26: In file included from src/PopSum.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/bootstrap.cc:21: In file included from src/bootstrap.h:26: In file included from src/PopSum.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/bootstrap.cc:21: In file included from src/bootstrap.h:26: In file included from src/PopSum.h:35: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/bootstrap.cc:21: In file included from src/bootstrap.h:26: In file included from src/PopSum.h:35: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/bootstrap.cc:21: In file included from src/bootstrap.h:26: In file included from src/PopSum.h:36: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: 19 warnings generated. In file included from src/Vcf.cc:23: In file included from src/Vcf.h:24: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/Vcf.cc:23: In file included from src/Vcf.h:24: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 4 warnings generated. In file included from src/mstack.cc:25: In file included from src/mstack.h:30: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/mstack.cc:25: In file included from src/mstack.h:30: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/mstack.cc:25: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: In file included from src/mstack.cc:26: In file included from src/models.h:28: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/mstack.cc:26: In file included from src/models.h:28: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/mstack.cc:26: src/models.h:115:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 115 | : alleles_(move(alleles)) | ^ | std:: src/models.h:117:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 117 | , sample_calls_(move(sample_calls)) | ^ | std:: src/models.h:124:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: src/models.h:124:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: 29 warnings generated. In file included from src/MetaPopInfo.cc:10: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/MetaPopInfo.cc:10: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: 4 warnings generated. In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/file_io.cc:25: In file included from src/file_io.h:41: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. In file included from src/Hwp.cc:21: In file included from src/Hwp.h:34: In file included from src/PopMap.h:35: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/Hwp.cc:21: In file included from src/Hwp.h:34: In file included from src/PopMap.h:35: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/Hwp.cc:21: In file included from src/Hwp.h:34: In file included from src/PopMap.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/Hwp.cc:21: In file included from src/Hwp.h:34: In file included from src/PopMap.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/Hwp.cc:21: In file included from src/Hwp.h:34: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: 19 warnings generated. In file included from src/models.cc:30: In file included from src/models.h:26: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:27: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:28: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:28: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/models.cc:30: In file included from src/models.h:29: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: In file included from src/models.cc:30: src/models.h:115:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 115 | : alleles_(move(alleles)) | ^ | std:: src/models.h:117:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 117 | , sample_calls_(move(sample_calls)) | ^ | std:: src/models.h:124:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: src/models.h:124:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: src/models.cc:515:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 515 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:515:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 515 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:709:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 709 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:709:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 709 | return SiteCall(move(allele_freqs), move(sample_calls)); | ^ | std:: src/models.cc:1007:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1007 | return SiteCall(move(allele_freqs), dimorph_qual, move(sample_calls)); | ^ | std:: src/models.cc:1007:55: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1007 | return SiteCall(move(allele_freqs), dimorph_qual, move(sample_calls)); | ^ | std:: 35 warnings generated. rm -f libclean.a ar cru libclean.a src/clean.o src/kmers.o src/file_io.o src/write.o ranlib libclean.a In file included from src/debruijn.cc:6: In file included from src/debruijn.h:12: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/debruijn.cc:6: In file included from src/debruijn.h:13: In file included from src/locus.h:32: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/debruijn.cc:6: In file included from src/debruijn.h:13: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/debruijn.cc:6: In file included from src/debruijn.h:13: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: src/debruijn.cc:451:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 451 | components.push_back(move(c.second)); | ^ | std:: 18 warnings generated. In file included from src/phasedstacks.cc:25: In file included from src/phasedstacks.h:46: In file included from src/catalog_utils.h:30: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/phasedstacks.cc:25: In file included from src/phasedstacks.h:46: In file included from src/catalog_utils.h:30: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/phasedstacks.cc:25: In file included from src/phasedstacks.h:46: In file included from src/catalog_utils.h:31: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/phasedstacks.cc:25: In file included from src/phasedstacks.h:46: In file included from src/catalog_utils.h:31: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/phasedstacks.cc:25: In file included from src/phasedstacks.h:46: In file included from src/catalog_utils.h:32: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: 19 warnings generated. In file included from src/mapping_utils.cc:25: In file included from src/mapping_utils.h:28: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/mapping_utils.cc:25: In file included from src/mapping_utils.h:28: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/mapping_utils.cc:25: In file included from src/mapping_utils.h:29: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/mapping_utils.cc:25: In file included from src/mapping_utils.h:29: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/mapping_utils.cc:25: In file included from src/mapping_utils.h:30: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: 19 warnings generated. In file included from src/locus.cc:24: In file included from src/locus.h:32: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/locus.cc:24: In file included from src/locus.h:32: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/locus.cc:24: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/locus.cc:24: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: src/locus.cc:519:51: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 519 | *r1 = SAlnRead(AlnRead::merger_of(move(*r1), move(*r2)), r1->sample); | ^ | std:: src/locus.cc:519:62: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 519 | *r1 = SAlnRead(AlnRead::merger_of(move(*r1), move(*r2)), r1->sample); | ^ | std:: src/locus.cc:668:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 668 | CLocAlnSet merged (move(left)); | ^ | std:: src/locus.cc:691:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 691 | merged.add(move(r)); | ^ | std:: src/locus.cc:727:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 727 | merged.add(move(r)); | ^ | std:: 22 warnings generated. In file included from src/process_shortreads.cc:27: In file included from src/process_shortreads.h:40: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/process_shortreads.cc:27: In file included from src/process_shortreads.h:40: In file included from src/clean.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/process_shortreads.cc:27: In file included from src/process_shortreads.h:40: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/process_shortreads.cc:27: In file included from src/process_shortreads.h:40: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/process_shortreads.cc:27: In file included from src/process_shortreads.h:40: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. In file included from src/clone_filter.cc:27: In file included from src/clone_filter.h:47: In file included from src/kmers.h:35: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/clone_filter.cc:27: In file included from src/clone_filter.h:47: In file included from src/kmers.h:35: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/clone_filter.cc:27: In file included from src/clone_filter.h:47: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/clone_filter.cc:27: In file included from src/clone_filter.h:47: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/clone_filter.cc:27: In file included from src/clone_filter.h:47: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. In file included from src/kmer_filter.cc:25: In file included from src/kmer_filter.h:49: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/kmer_filter.cc:25: In file included from src/kmer_filter.h:49: In file included from src/clean.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/kmer_filter.cc:25: In file included from src/kmer_filter.h:49: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/kmer_filter.cc:25: In file included from src/kmer_filter.h:49: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/kmer_filter.cc:25: In file included from src/kmer_filter.h:49: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:30: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:30: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:31: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:31: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:32: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: 19 warnings generated. 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 ranlib libcore.a c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o process_shortreads src/process_shortreads.o htslib/libhts.a libcore.a libclean.a -lz -lgomp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o phasedstacks src/phasedstacks.o htslib/libhts.a libcore.a -lz -lgomp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o clone_filter src/clone_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o kmer_filter src/kmer_filter.o htslib/libhts.a libcore.a libclean.a -lz -lgomp In file included from src/PopSum.cc:21: In file included from src/PopSum.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/PopSum.cc:21: In file included from src/PopSum.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/PopSum.cc:21: In file included from src/PopSum.h:35: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/PopSum.cc:21: In file included from src/PopSum.h:35: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/PopSum.cc:21: In file included from src/PopSum.h:36: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: 19 warnings generated. In file included from src/ustacks.cc:25: In file included from src/ustacks.h:53: In file included from src/kmers.h:35: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/ustacks.cc:25: In file included from src/ustacks.h:53: In file included from src/kmers.h:35: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/ustacks.cc:25: In file included from src/ustacks.h:53: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/ustacks.cc:25: In file included from src/ustacks.h:53: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/ustacks.cc:25: In file included from src/ustacks.h:53: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: In file included from src/ustacks.cc:25: In file included from src/ustacks.h:59: src/models.h:115:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 115 | : alleles_(move(alleles)) | ^ | std:: src/models.h:117:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 117 | , sample_calls_(move(sample_calls)) | ^ | std:: src/models.h:124:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: src/models.h:124:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: In file included from src/ustacks.cc:25: In file included from src/ustacks.h:65: src/GappedAln.h:42:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 42 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:49:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 49 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:778:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 778 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len))); | ^ | std:: src/GappedAln.h:924:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 924 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len), (uint) j)); | ^ | std:: 33 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o ustacks src/ustacks.o htslib/libhts.a libcore.a -lz -lgomp In file included from src/sstacks.cc:29: In file included from src/catalog_utils.h:30: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/sstacks.cc:29: In file included from src/catalog_utils.h:30: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/sstacks.cc:29: In file included from src/catalog_utils.h:31: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/sstacks.cc:29: In file included from src/catalog_utils.h:31: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/sstacks.cc:29: In file included from src/catalog_utils.h:32: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: In file included from src/sstacks.cc:34: In file included from src/sstacks.h:50: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: In file included from src/sstacks.cc:34: In file included from src/sstacks.h:53: src/GappedAln.h:42:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 42 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:49:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 49 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:778:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 778 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len))); | ^ | std:: src/GappedAln.h:924:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 924 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len), (uint) j)); | ^ | std:: 31 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o sstacks src/sstacks.o htslib/libhts.a libcore.a -lz -lgomp In file included from src/process_radtags.cc:31: In file included from src/process_radtags.h:43: In file included from src/clean.h:30: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/process_radtags.cc:31: In file included from src/process_radtags.h:43: In file included from src/clean.h:30: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/process_radtags.cc:31: In file included from src/process_radtags.h:43: In file included from src/clean.h:31: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/process_radtags.cc:31: In file included from src/process_radtags.h:43: In file included from src/clean.h:31: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/process_radtags.cc:31: In file included from src/process_radtags.h:43: In file included from src/clean.h:31: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: 25 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o process_radtags src/process_radtags.o htslib/libhts.a libcore.a libclean.a -lz -lgomp In file included from src/tsv2bam.cc:29: In file included from src/sql_utilities.h:29: In file included from src/input.h:34: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/tsv2bam.cc:29: In file included from src/sql_utilities.h:29: In file included from src/input.h:34: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/tsv2bam.cc:31: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/tsv2bam.cc:31: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/tsv2bam.cc:38: In file included from src/catalog_utils.cc:32: In file included from src/catalog_utils.h:32: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: src/tsv2bam.cc:358:45: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 358 | readname_to_loc.insert({move(read_name2), &loc.second}); | ^ | std:: src/tsv2bam.cc:381:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 381 | stack.second.push_back(move(id)); | ^ | std:: 21 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o tsv2bam src/tsv2bam.o htslib/libhts.a libcore.a -lz -lgomp In file included from src/cstacks.cc:26: In file included from src/cstacks.h:50: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/cstacks.cc:26: In file included from src/cstacks.h:50: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/cstacks.cc:26: In file included from src/cstacks.h:51: In file included from src/kmers.h:36: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/cstacks.cc:26: In file included from src/cstacks.h:51: In file included from src/kmers.h:36: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/cstacks.cc:26: In file included from src/cstacks.h:51: In file included from src/kmers.h:37: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: In file included from src/cstacks.cc:26: In file included from src/cstacks.h:53: src/GappedAln.h:42:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 42 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:49:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 49 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:778:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 778 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len))); | ^ | std:: src/GappedAln.h:924:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 924 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len), (uint) j)); | ^ | std:: 29 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o cstacks src/cstacks.o htslib/libhts.a libcore.a -lz -lgomp In file included from src/export_formats.cc:24: In file included from src/export_formats.h:29: In file included from src/locus.h:32: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/export_formats.cc:24: In file included from src/export_formats.h:29: In file included from src/locus.h:32: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/export_formats.cc:24: In file included from src/export_formats.h:29: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/export_formats.cc:24: In file included from src/export_formats.h:29: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/export_formats.cc:24: In file included from src/export_formats.h:30: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: src/export_formats.cc:2668:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2668 | this->_writer = new VcfWriter(this->_path, move(header)); | ^ | std:: src/export_formats.cc:2780:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2780 | this->_writer = new VcfWriter(this->_path, move(header)); | ^ | std:: src/export_formats.cc:2886:48: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 2886 | this->_writer = new VcfWriter(this->_path, move(header)); | ^ | std:: 22 warnings generated. rm -f libpop.a ar cru libpop.a src/bootstrap.o src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o ranlib libpop.a In file included from src/populations.cc:29: In file included from src/populations.h:46: In file included from src/stacks.h:40: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/populations.cc:29: In file included from src/populations.h:46: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/populations.cc:29: In file included from src/populations.h:47: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/populations.cc:29: In file included from src/populations.h:47: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/populations.cc:29: In file included from src/populations.h:49: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: In file included from src/populations.cc:29: In file included from src/populations.h:62: src/locus_readers.h:232:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 232 | readgroups_per_f[bam_f_i].push_back({move(rg), move(name), stacks_id}); | ^ | std:: src/locus_readers.h:232:64: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 232 | readgroups_per_f[bam_f_i].push_back({move(rg), move(name), stacks_id}); | ^ | std:: src/locus_readers.h:367:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 367 | bam_fs_(move(bam_fs)), | ^ | std:: src/locus_readers.h:496:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 496 | bam_fs_(move(bam_fs)), | ^ | std:: src/locus_readers.h:661:32: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 661 | std::make_pair(move(rec_5prime_pos), vector>()) | ^ | std:: src/locus_readers.h:663:38: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 663 | locus_itr->second.push_back({move(rec), sample}); | ^ | std:: src/locus_readers.h:666:32: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 666 | std::make_pair(move(rec_5prime_pos), std::make_pair(move(rec), move(sample))) | ^ | std:: src/locus_readers.h:666:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 666 | std::make_pair(move(rec_5prime_pos), std::make_pair(move(rec), move(sample))) | ^ | std:: src/locus_readers.h:666:80: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 666 | std::make_pair(move(rec_5prime_pos), std::make_pair(move(rec), move(sample))) | ^ | std:: src/locus_readers.h:871:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 871 | fw_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), sample)); | ^ | std:: src/locus_readers.h:871:61: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 871 | fw_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), sample)); | ^ | std:: src/locus_readers.h:871:74: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 871 | fw_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), sample)); | ^ | std:: src/locus_readers.h:951:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 951 | pe_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), pe_sample)); | ^ | std:: src/locus_readers.h:951:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 951 | pe_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), pe_sample)); | ^ | std:: src/locus_readers.h:951:78: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 951 | pe_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), pe_sample)); | ^ | std:: src/locus_readers.h:964:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 964 | aln_loc.add(move(read)); | ^ | std:: src/locus_readers.h:968:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 968 | aln_loc.add(move(read)); | ^ | std:: src/locus_readers.h:1014:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1014 | records.push_back(move(next_rec_)); | ^ | std:: src/locus_readers.h:1027:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1027 | next_rec_ = move(records.back()); | ^ | std:: In file included from src/populations.cc:29: In file included from src/populations.h:49: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/populations.cc:745:26: note: in instantiation of member function 'PopMap::populate_internal' requested here 745 | PopMap::populate_internal( | ^ In file included from src/populations.cc:29: In file included from src/populations.h:49: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: 40 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o populations src/populations.o htslib/libhts.a libcore.a libpop.a -lz -lgomp In file included from src/gstacks.cc:23: In file included from src/gstacks.h:25: In file included from src/models.h:26: src/DNASeq4.h:80:58: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 80 | DNASeq4(DNASeq4&& other) noexcept : l_(other.l_), v_(move(other.v_)) {other.clear();} | ^ | std:: src/DNASeq4.h:86:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 86 | DNASeq4& operator= (DNASeq4&& other) {l_ = other.l_; v_ = move(other.v_); other.clear(); return *this;} | ^ | std:: In file included from src/gstacks.cc:23: In file included from src/gstacks.h:25: In file included from src/models.h:27: src/stacks.h:270:15: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: src/stacks.h:270:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 270 | : seq(move(s)), name(move(n)) | ^ | std:: In file included from src/gstacks.cc:23: In file included from src/gstacks.h:25: In file included from src/models.h:28: In file included from src/locus.h:34: src/Alignment.h:59:41: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:59:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 59 | AlnRead(Read&& r, Cigar&& c) : Read(move(r)), cigar(move(c)) {} | ^ | std:: src/Alignment.h:223:25: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:36: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: src/Alignment.h:223:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 223 | return AlnRead(Read(move(seq), move(name)), move(cig)); | ^ | std:: In file included from src/gstacks.cc:23: In file included from src/gstacks.h:25: In file included from src/models.h:28: src/locus.h:180:40: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 180 | SRead(Read&& r, size_t spl) : Read(move(r)), sample(spl) {} | ^ | std:: src/locus.h:186:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 186 | SAlnRead(AlnRead&& r, size_t spl) : AlnRead(move(r)), sample(spl) {} | ^ | std:: src/locus.h:187:57: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:187:66: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 187 | SAlnRead(Read&& r, Cigar&& c, size_t spl) : AlnRead(move(r), move(c)), sample(spl) {} | ^ | std:: src/locus.h:216:43: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 216 | void add(SRead&& r) {reads_.push_back(move(r));} | ^ | std:: src/locus.h:217:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 217 | void add_pe(SRead&& r) {pe_reads_.push_back(move(r));} | ^ | std:: src/locus.h:245:35: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 245 | void ref(DNASeq4&& s) {ref_ = move(s);} | ^ | std:: src/locus.h:308:22: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 308 | reads_.push_back(move(r)); | ^ | std:: In file included from src/gstacks.cc:23: In file included from src/gstacks.h:25: In file included from src/models.h:29: src/mstack.h:92:18: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 92 | , utags (move(o.utags)) | ^ | std:: src/mstack.h:93:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 93 | , remtags (move(o.remtags)) | ^ | std:: src/mstack.h:95:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 95 | , dist (move(o.dist)) | ^ | std:: src/mstack.h:96:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 96 | , alns (move(o.alns)) | ^ | std:: src/mstack.h:99:16: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 99 | , loc (move(o.loc)) | ^ | std:: src/mstack.h:100:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 100 | , snps (move(o.snps)) | ^ | std:: src/mstack.h:101:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 101 | , alleles (move(o.alleles)) | ^ | std:: src/mstack.h:102:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 102 | , gaps (move(o.gaps)) | ^ | std:: In file included from src/gstacks.cc:23: In file included from src/gstacks.h:25: src/models.h:115:24: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 115 | : alleles_(move(alleles)) | ^ | std:: src/models.h:117:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 117 | , sample_calls_(move(sample_calls)) | ^ | std:: src/models.h:124:20: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: src/models.h:124:39: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 124 | : SiteCall(move(alleles), -1, move(sample_calls)) {} | ^ | std:: In file included from src/gstacks.cc:23: In file included from src/gstacks.h:27: src/GappedAln.h:42:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 42 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:49:28: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 49 | this->cigar = move(cigar); | ^ | std:: src/GappedAln.h:778:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 778 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len))); | ^ | std:: src/GappedAln.h:924:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 924 | alns.push_back(AlignRes(move(cigar), gaps, contiguity, (ident / (double) len), (uint) j)); | ^ | std:: In file included from src/gstacks.cc:23: In file included from src/gstacks.h:30: src/locus_readers.h:232:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 232 | readgroups_per_f[bam_f_i].push_back({move(rg), move(name), stacks_id}); | ^ | std:: src/locus_readers.h:232:64: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 232 | readgroups_per_f[bam_f_i].push_back({move(rg), move(name), stacks_id}); | ^ | std:: src/locus_readers.h:367:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 367 | bam_fs_(move(bam_fs)), | ^ | std:: src/locus_readers.h:496:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 496 | bam_fs_(move(bam_fs)), | ^ | std:: src/locus_readers.h:661:32: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 661 | std::make_pair(move(rec_5prime_pos), vector>()) | ^ | std:: src/locus_readers.h:663:38: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 663 | locus_itr->second.push_back({move(rec), sample}); | ^ | std:: src/locus_readers.h:666:32: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 666 | std::make_pair(move(rec_5prime_pos), std::make_pair(move(rec), move(sample))) | ^ | std:: src/locus_readers.h:666:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 666 | std::make_pair(move(rec_5prime_pos), std::make_pair(move(rec), move(sample))) | ^ | std:: src/locus_readers.h:666:80: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 666 | std::make_pair(move(rec_5prime_pos), std::make_pair(move(rec), move(sample))) | ^ | std:: src/locus_readers.h:871:50: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 871 | fw_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), sample)); | ^ | std:: src/locus_readers.h:871:61: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 871 | fw_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), sample)); | ^ | std:: src/locus_readers.h:871:74: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 871 | fw_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), sample)); | ^ | std:: src/locus_readers.h:951:54: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 951 | pe_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), pe_sample)); | ^ | std:: src/locus_readers.h:951:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 951 | pe_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), pe_sample)); | ^ | std:: src/locus_readers.h:951:78: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 951 | pe_reads.push_back(SAlnRead(AlnRead(Read(move(seq), move(name)), move(cigar)), pe_sample)); | ^ | std:: src/locus_readers.h:964:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 964 | aln_loc.add(move(read)); | ^ | std:: src/locus_readers.h:968:21: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 968 | aln_loc.add(move(read)); | ^ | std:: src/locus_readers.h:1014:23: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1014 | records.push_back(move(next_rec_)); | ^ | std:: src/locus_readers.h:1027:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1027 | next_rec_ = move(records.back()); | ^ | std:: In file included from src/gstacks.cc:29: In file included from src/catalog_utils.h:32: src/PopMap.h:452:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 452 | ++cloc->alleles[move(hap)]; | ^ | std:: src/PopMap.h:454:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 454 | ++cloc->alleles[move(hap)]; | ^ | std:: src/gstacks.cc:156:49: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 156 | bam_cloc_reader.reset(new BamCLocReader(move(bam_f_ptrs))); | ^ | std:: src/gstacks.cc:162:51: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 162 | bam_cloc_builder.reset(new BamCLocBuilder(move(bam_f_ptrs), refbased_cfg, sample_names)); | ^ | std:: src/gstacks.cc:201:60: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 201 | o_vcf_f.reset(new VcfWriter(out_dir + "catalog.calls", move(vcf_header))); | ^ | std:: src/gstacks.cc:347:63: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 347 | fa_outputs[loc_i - next_fa_to_write] = {true, move(loc_proc.fasta_out())}; | ^ | std:: src/gstacks.cc:365:65: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 365 | vcf_outputs[loc_i - next_vcf_to_write] = {true, move(loc_proc.vcf_out()) }; | ^ | std:: src/gstacks.cc:393:78: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 393 | bam_outputs[loc_i - next_bam_to_write] = make_pair(true, move(loc_proc.bam_out())); | ^ | std:: src/gstacks.cc:417:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 417 | det_outputs[loc_i - next_det_to_write] = {true, move(loc_proc.details_out())}; | ^ | std:: src/gstacks.cc:1027:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1027 | aln_loc.ref(move(ctg)); | ^ | std:: src/gstacks.cc:1056:29: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1056 | aln_loc.ref(move(new_ctg)); | ^ | std:: src/gstacks.cc:1079:46: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1079 | if(add_read_to_aln(aln_loc, aln_res, move(r), &aligner, stree)) { | ^ | std:: src/gstacks.cc:1093:47: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1093 | if (add_read_to_aln(aln_loc, aln_res, move(r), &aligner, stree)) { | ^ | std:: src/gstacks.cc:1160:69: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1160 | loc_.o_bam.at(merged_input ? 0 : read.sample).push_back(move(rec)); | ^ | std:: src/gstacks.cc:1309:17: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1309 | aln_loc.ref(move(consensus)); | ^ | std:: src/gstacks.cc:1799:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1799 | fw_contig = move(contig); | ^ | std:: src/gstacks.cc:1805:33: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1805 | pe_contig = move(contig); | ^ | std:: src/gstacks.cc:1855:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1855 | contig = move(fw_contig); | ^ | std:: src/gstacks.cc:1866:30: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1866 | contig = move(fw_contig); | ^ | std:: src/gstacks.cc:1895:26: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1895 | aln_loc.add(SAlnRead(move((Read&)r), move(cigar), r.sample)); | ^ | std:: src/gstacks.cc:1895:42: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] 1895 | aln_loc.add(SAlnRead(move((Read&)r), move(cigar), r.sample)); | ^ | std:: 73 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -lpthread -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o htslib/libhts.a libcore.a -lz -lgomp gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> stacks-2.68 depends on file: /usr/local/bin/python3.11 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for stacks-2.68 ===> Generating temporary packing list Making install in htslib gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68/htslib' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68/htslib' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68/htslib' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68/htslib' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' /bin/mkdir -p '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' install -s -m 555 ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' install -m 555 scripts/denovo_map.pl scripts/ref_map.pl scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-private-alleles scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin' /usr/local/bin/gmake install-data-hook gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' sed -e 's,_VERSION_,2.68,' -e 's,_BINDIR_,/usr/local/bin/,g' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl > /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl.subst mv /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl.subst /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/denovo_map.pl sed -e 's,_VERSION_,2.68,' -e 's,_BINDIR_,/usr/local/bin/,g' -e 's,_PKGDATADIR_,/usr/local/share/stacks/,g' /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl > /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl.subst mv /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl.subst /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.68,' /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.68,' /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-samtools-tview rm -f /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-integrate-alignments.bkp rm -f /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-samtools-tview.bkp chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-integrate-alignments chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-dist-extract chmod +x /wrkdirs/usr/ports/biology/stacks/work/stage/usr/local/bin/stacks-gdb gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stacks/work/stacks-2.68' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-01-20T21:28:40+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=989b3863994b' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for stacks-2.68 ===> Building stacks-2.68 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for stacks-2.68 build of biology/stacks | stacks-2.68 ended at Tue Jan 20 16:31:53 EST 2026 build time: 00:03:16