=>> Building biology/vt build started at Sun Nov 9 18:29:54 EST 2025 port directory: /usr/ports/biology/vt package name: vt-0.57721_3 building for: FreeBSD pkg.DaveG.ca 15.0-ALPHA3 FreeBSD 15.0-ALPHA3 1500064 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 541 Aug 27 2024 /usr/ports/biology/vt/Makefile Ports top last git commit: ec159283c191 Ports top unclean checkout: no Port dir last git commit: 173b9df467e9 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500064 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500064 UNAME_v=FreeBSD 15.0-ALPHA3 1500064 UNAME_r=15.0-ALPHA3 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_15_c_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_15_c_x64-HEAD-ALL/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_c_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_c_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-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vt/work/.cache HOME=/wrkdirs/usr/ports/biology/vt/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vt/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vt/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- OPENSSLBASE=/usr OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vt/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vt/work/.cache HOME=/wrkdirs/usr/ports/biology/vt/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vt/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vt/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=" " 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-- OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/vt" EXAMPLESDIR="share/examples/vt" DATADIR="share/vt" WWWDIR="www/vt" ETCDIR="etc/vt" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vt DOCSDIR=/usr/local/share/doc/vt EXAMPLESDIR=/usr/local/share/examples/vt WWWDIR=/usr/local/www/vt ETCDIR=/usr/local/etc/vt --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 ===> vt-0.57721_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_1: .......... done ===> vt-0.57721_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vt-0.57721_3 =========================================================================== =================================================== ===== 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 vt-0.57721_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by vt-0.57721_3 for building => SHA256 Checksum OK for atks-vt-0.57721_GH0.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 vt-0.57721_3 for building ===> Extracting for vt-0.57721_3 => SHA256 Checksum OK for atks-vt-0.57721_GH0.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 vt-0.57721_3 ===> Applying FreeBSD patches for vt-0.57721_3 from /usr/ports/biology/vt/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vt-0.57721_3 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-0.23.1... [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-0.23.1: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> vt-0.57721_3 depends on package: gmake>=4.4.1 - found ===> Returning to build of vt-0.57721_3 ===> vt-0.57721_3 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. ===> vt-0.57721_3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of vt-0.57721_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> vt-0.57721_3 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.22.pkg [pkg.DaveG.ca] Installing htslib-1.22... [pkg.DaveG.ca] `-- Installing curl-8.16.0... [pkg.DaveG.ca] | `-- Installing brotli-1.1.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.1.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.1... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.1: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7... [pkg.DaveG.ca] | | `-- Installing liblz4-1.10.0_2,1... [pkg.DaveG.ca] | | `-- Extracting liblz4-1.10.0_2,1: .......... done [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.16.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.24... [pkg.DaveG.ca] `-- Extracting libdeflate-1.24: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... done ===> vt-0.57721_3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of vt-0.57721_3 ===> vt-0.57721_3 depends on shared library: libsvm.so - not found ===> Installing existing package /packages/All/libsvm-3.24.pkg [pkg.DaveG.ca] Installing libsvm-3.24... [pkg.DaveG.ca] Extracting libsvm-3.24: .......... done ===== Message from libsvm-3.24: -- Some useful tools are installed to /usr/local/share/libsvm. Most of them are written in Python, please install lang/python before trying them. -- ===> NOTICE: The libsvm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> vt-0.57721_3 depends on shared library: libsvm.so - found (/usr/local/lib/libsvm.so) ===> Returning to build of vt-0.57721_3 ===> vt-0.57721_3 depends on shared library: libdeflate.so - found (/usr/local/lib/libdeflate.so) ===> vt-0.57721_3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for vt-0.57721_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for vt-0.57721_3 cd lib/Rmath; /usr/local/bin/gmake libRmath.a || exit 1; cd lib/pcre2; /usr/local/bin/gmake libpcre2.a || exit 1; c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ahmm.o -c ahmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o align.o -c align.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o allele.o -c allele.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_1000g.o -c annotate_1000g.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_dbsnp_rsid.o -c annotate_dbsnp_rsid.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_indels.o -c annotate_indels.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_indels2.o -c annotate_indels2.cpp gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/Rmath' c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_regions.o -c annotate_regions.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_variants.o -c annotate_variants.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o annotate_vntrs.o -c annotate_vntrs.cpp gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/pcre2' cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_auto_possess.o -c pcre2_auto_possess.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o augmented_bam_record.o -c augmented_bam_record.cpp cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_chartables.o -c pcre2_chartables.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_compile.o -c pcre2_compile.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_genotyping_buffered_reader.o -c bcf_genotyping_buffered_reader.cpp cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_config.o -c pcre2_config.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_single_genotyping_buffered_reader.o -c bcf_single_genotyping_buffered_reader.cpp cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_context.o -c pcre2_context.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bam_ordered_reader.o -c bam_ordered_reader.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bd0.c -o bd0.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnbeta.c -o dnbeta.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_dfa_match.o -c pcre2_dfa_match.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bcf_synced_reader.o -c bcf_synced_reader.cpp cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_error.o -c pcre2_error.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_jit_compile.o -c pcre2_jit_compile.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_maketables.o -c pcre2_maketables.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match.o -c pcre2_match.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o bed.o -c bed.cpp cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match_data.o -c pcre2_match_data.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c i1mach.c -o i1mach.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_newline.o -c pcre2_newline.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ord2utf.o -c pcre2_ord2utf.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnbinom.c -o pnbinom.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o candidate_motif_picker.o -c candidate_motif_picker.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qlnorm.c -o qlnorm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_pattern_info.o -c pcre2_pattern_info.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o candidate_region_extractor.o -c candidate_region_extractor.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o cat.o -c cat.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o chmm.o -c chmm.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rgeom.c -o rgeom.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_string_utils.o -c pcre2_string_utils.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_i.c -o bessel_i.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnbinom.c -o dnbinom.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o complex_genotyping_record.o -c complex_genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_concordance.o -c compute_concordance.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_features.o -c compute_features.cpp cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_study.o -c pcre2_study.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c imax2.c -o imax2.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_features2.o -c compute_features2.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o compute_rl_dist.o -c compute_rl_dist.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o config.o -c config.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate_multiallelics.o -c consolidate_multiallelics.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate_vntrs.o -c consolidate_vntrs.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnchisq.c -o pnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qlogis.c -o qlogis.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rhyper.c -o rhyper.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substitute.o -c pcre2_substitute.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_j.c -o bessel_j.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnchisq.c -o dnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c imin2.c -o imin2.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substring.o -c pcre2_substring.c c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o consolidate.o -c consolidate.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o construct_probes.o -c construct_probes.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnf.c -o pnf.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_tables.o -c pcre2_tables.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ucd.o -c pcre2_ucd.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnbeta.c -o qnbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rlnorm.c -o rlnorm.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_valid_utf.o -c pcre2_valid_utf.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_k.c -o bessel_k.o cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_xclass.o -c pcre2_xclass.c cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnf.c -o dnf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c lbeta.c -o lbeta.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose.o -c decompose.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnorm.c -o pnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnbinom.c -o qnbinom.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose2.o -c decompose2.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rlogis.c -o rlogis.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c bessel_y.c -o bessel_y.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o decompose_blocksub.o -c decompose_blocksub.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnorm.c -o dnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c lgamma.c -o lgamma.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o discover.o -c discover.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnt.c -o pnt.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o duplicate.o -c duplicate.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnchisq.c -o qnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rmultinom.c -o rmultinom.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o estimate.o -c estimate.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c beta.c -o beta.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o estimator.o -c estimator.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dnt.c -o dnt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c lgammacor.c -o lgammacor.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c polygamma.c -o polygamma.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o extract_vntrs.o -c extract_vntrs.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnf.c -o qnf.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o filter.o -c filter.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rnbinom.c -o rnbinom.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o filter_overlap.o -c filter_overlap.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c chebyshev.c -o chebyshev.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o flank_detector.o -c flank_detector.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o fuzzy_aligner.o -c fuzzy_aligner.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dpois.c -o dpois.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c log1p.c -o log1p.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o fuzzy_partition.o -c fuzzy_partition.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o gencode.o -c gencode.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c ppois.c -o ppois.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genome_interval.o -c genome_interval.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnorm.c -o qnorm.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genotype.o -c genotype.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o genotyping_record.o -c genotyping_record.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rnchisq.c -o rnchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c choose.c -o choose.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dt.c -o dt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c mlutils.c -o mlutils.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pt.c -o pt.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ghmm.o -c ghmm.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qnt.c -o qnt.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o hts_utils.o -c hts_utils.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rnorm.c -o rnorm.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c d1mach.c -o d1mach.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dunif.c -o dunif.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pbeta.c -o pbeta.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o hfilter.o -c hfilter.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c ptukey.c -o ptukey.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o indel_annotator.o -c indel_annotator.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qpois.c -o qpois.o bcf_ordered_writer.cpp:128:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 128 | bcf_hdr_write(file, hdr); | ^~~~~~~~~~~~~ ~~~~~~~~~ bcf_ordered_writer.cpp:167:43: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 161 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~~ | %ld 162 | __FILE__, 163 | __LINE__, 164 | __FUNCTION__, 165 | window, 166 | bcf_get_chrom(hdr, v), 167 | bcf_get_pos1(v), | ^~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' 464 | #define bcf_get_pos1(v) ((v)->pos+1) | ^~~~~~~~~~~~ bcf_ordered_writer.cpp:169:43: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 161 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~~ | %ld 162 | __FILE__, 163 | __LINE__, 164 | __FUNCTION__, 165 | window, 166 | bcf_get_chrom(hdr, v), 167 | bcf_get_pos1(v), 168 | cutoff_pos1, 169 | bcf_get_pos1(buffer.front()), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' 464 | #define bcf_get_pos1(v) ((v)->pos+1) | ^~~~~~~~~~~~ bcf_ordered_writer.cpp:171:43: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 161 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~~ | %ld 162 | __FILE__, 163 | __LINE__, 164 | __FUNCTION__, 165 | window, 166 | bcf_get_chrom(hdr, v), 167 | bcf_get_pos1(v), 168 | cutoff_pos1, 169 | bcf_get_pos1(buffer.front()), 170 | window, 171 | bcf_get_pos1(buffer.front())-bcf_get_pos1(v)+1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' 464 | #define bcf_get_pos1(v) ((v)->pos+1) | ^ bcf_ordered_writer.cpp:194:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 194 | bcf_write(file, hdr, v); | ^~~~~~~~~ ~~~~~~~~~~~~ bcf_ordered_writer.cpp:244:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 244 | bcf_write(file, hdr, buffer.back()); | ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ bcf_ordered_writer.cpp:260:21: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 260 | bcf_write(file, hdr, buffer.back()); | ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ 7 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o indel_genotyping_record.o -c indel_genotyping_record.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rpois.c -o rpois.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dbeta.c -o dbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dweibull.c -o dweibull.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o index.o -c index.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o info2tab.o -c info2tab.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o interval_tree.o -c interval_tree.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pbinom.c -o pbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c punif.c -o punif.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qt.c -o qt.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rt.c -o rt.o ar -rc libpcre2.a pcre2_auto_possess.o pcre2_chartables.o pcre2_compile.o pcre2_config.o pcre2_context.o pcre2_dfa_match.o pcre2_error.o pcre2_jit_compile.o pcre2_maketables.o pcre2_match.o pcre2_match_data.o pcre2_newline.o pcre2_ord2utf.o pcre2_pattern_info.o pcre2_string_utils.o pcre2_study.o pcre2_substitute.o pcre2_substring.o pcre2_tables.o pcre2_ucd.o pcre2_valid_utf.o pcre2_xclass.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dbinom.c -o dbinom.o ranlib libpcre2.a cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c expm1.c -o expm1.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o interval.o -c interval.cpp gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/pcre2' bcf_genotyping_buffered_reader.cpp:2110:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 2110 | float pG[no_genotypes]; | ^~~~~~~~~~~~ bcf_genotyping_buffered_reader.cpp:2110:18: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression bcf_genotyping_buffered_reader.cpp:2108:17: note: declared here 2108 | int32_t no_genotypes = (no_alleles * (no_alleles+1)) >> 1; | ^ 1 warning generated. cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pcauchy.c -o pcauchy.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pweibull.c -o pweibull.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o lfhmm.o -c lfhmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o lhmm.o -c lhmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o lhmm1.o -c lhmm1.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o liftover.o -c liftover.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qtukey.c -o qtukey.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o log_tool.o -c log_tool.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c runif.c -o runif.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o merge.o -c merge.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dcauchy.c -o dcauchy.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fmax2.c -o fmax2.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pchisq.c -o pchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qbeta.c -o qbeta.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o merge_candidate_variants.o -c merge_candidate_variants.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o merge_genotypes.o -c merge_genotypes.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qunif.c -o qunif.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o milk_filter.o -c milk_filter.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rweibull.c -o rweibull.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o motif_tree.o -c motif_tree.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dchisq.c -o dchisq.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fmin2.c -o fmin2.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o motif_map.o -c motif_map.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pexp.c -o pexp.o estimator.cpp:120:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 120 | int32_t gt_indiv[ploidy]; | ^~~~~~ estimator.cpp:120:26: note: function parameter 'ploidy' with unknown value cannot be used in a constant expression estimator.cpp:41:70: note: declared here 41 | void Estimator::compute_af(int32_t *gts, int32_t no_samples, int32_t ploidy, | ^ estimator.cpp:193:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 193 | int32_t imap[no_samples]; | ^~~~~~~~~~ estimator.cpp:193:22: note: function parameter 'no_samples' with unknown value cannot be used in a constant expression estimator.cpp:179:57: note: declared here 179 | void Estimator::compute_gl_af_hwe(int32_t *pls, int32_t no_samples, int32_t ploidy, | ^ estimator.cpp:261:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 261 | int32_t imap[no_samples]; | ^~~~~~~~~~ estimator.cpp:261:22: note: function parameter 'no_samples' with unknown value cannot be used in a constant expression estimator.cpp:179:57: note: declared here 179 | void Estimator::compute_gl_af_hwe(int32_t *pls, int32_t no_samples, int32_t ploidy, | ^ estimator.cpp:274:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 274 | float af[no_alleles]; | ^~~~~~~~~~ estimator.cpp:274:18: note: function parameter 'no_alleles' with unknown value cannot be used in a constant expression estimator.cpp:180:25: note: declared here 180 | int32_t no_alleles, float *MLE_HWE_AF, float *MLE_HWE_GF, int32_t& n, | ^ estimator.cpp:280:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 280 | float gf[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:280:18: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:262:17: note: declared here 262 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimator.cpp:281:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 281 | float gf_indiv[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:281:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:262:17: note: declared here 262 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimator.cpp:369:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 369 | int32_t imap[nsamples]; | ^~~~~~~~ estimator.cpp:369:22: note: function parameter 'nsamples' with unknown value cannot be used in a constant expression estimator.cpp:360:53: note: declared here 360 | void Estimator::compute_gl_af(int32_t *pls, int32_t nsamples, int32_t ploidy, | ^ estimator.cpp:439:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 439 | int32_t imap[nsamples]; | ^~~~~~~~ estimator.cpp:439:22: note: function parameter 'nsamples' with unknown value cannot be used in a constant expression estimator.cpp:360:53: note: declared here 360 | void Estimator::compute_gl_af(int32_t *pls, int32_t nsamples, int32_t ploidy, | ^ estimator.cpp:452:18: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 452 | float gf[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:452:18: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:440:17: note: declared here 440 | int32_t no_genotypes = bcf_an2gn(n_allele); | ^ estimator.cpp:453:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 453 | float gf_indiv[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:453:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:440:17: note: declared here 440 | int32_t no_genotypes = bcf_an2gn(n_allele); | ^ estimator.cpp:667:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 667 | float HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ estimator.cpp:667:22: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimator.cpp:665:17: note: declared here 665 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 11 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o multi_partition.o -c multi_partition.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qbinom.c -o qbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qweibull.c -o qweibull.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dexp.c -o dexp.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o multiallelics_consolidator.o -c multiallelics_consolidator.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fprec.c -o fprec.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pf.c -o pf.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o needle.o -c needle.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o normalize.o -c normalize.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qcauchy.c -o qcauchy.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o nuclear_pedigree.o -c nuclear_pedigree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ordered_bcf_overlap_matcher.o -c ordered_bcf_overlap_matcher.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rbeta.c -o rbeta.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o partition.o -c partition.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sign.c -o sign.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o paste.o -c paste.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c df.c -o df.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fround.c -o fround.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pgamma.c -o pgamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qchisq.c -o qchisq.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o paste_genotypes.o -c paste_genotypes.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o pedigree.o -c pedigree.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rbinom.c -o rbinom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c signrank.c -o signrank.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o peek.o -c peek.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o pileup.o -c pileup.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o pregex.o -c pregex.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dgamma.c -o dgamma.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c fsign.c -o fsign.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pgeom.c -o pgeom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qexp.c -o qexp.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_afs.o -c profile_afs.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_chm1.o -c profile_chm1.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rcauchy.c -o rcauchy.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dgeom.c -o dgeom.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_chrom.o -c profile_chrom.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_fic_hwe.o -c profile_fic_hwe.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_hwe.o -c profile_hwe.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c ftrunc.c -o ftrunc.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c phyper.c -o phyper.o compute_features.cpp:217:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 217 | int32_t g[ploidy]; | ^~~~~~ compute_features.cpp:217:23: note: read of non-const variable 'ploidy' is not allowed in a constant expression compute_features.cpp:193:21: note: declared here 193 | int32_t ploidy = bcf_get_genotypes(odr->hdr, v, >s, &n_gts); | ^ compute_features.cpp:219:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 219 | int32_t AC[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:219:24: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:220:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 220 | float AF[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:220:22: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:225:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 225 | int32_t GC[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:225:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features.cpp:227:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 227 | float GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:227:22: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features.cpp:247:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 247 | float MLE_HWE_AF[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:247:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:248:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 248 | float MLE_HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:248:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features.cpp:258:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 258 | float MLE_AF[no_alleles]; | ^~~~~~~~~~ compute_features.cpp:258:26: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features.cpp:202:21: note: declared here 202 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features.cpp:259:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 259 | float MLE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features.cpp:259:26: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features.cpp:224:21: note: declared here 224 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 9 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_indels.o -c profile_indels.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_len.o -c profile_len.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qf.c -o qf.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_mendelian.o -c profile_mendelian.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rchisq.c -o rchisq.o hts_utils.cpp:428:21: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 428 | if ( h->dirty ) bcf_hdr_sync(h); | ^~~~~~~~~~~~ ~ hts_utils.cpp:443:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 443 | int len[m]; | ^ hts_utils.cpp:443:13: note: read of non-const variable 'm' is not allowed in a constant expression hts_utils.cpp:441:14: note: declared here 441 | int tid, m = kh_size(d); | ^ 2 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_na12878.o -c profile_na12878.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c stirlerr.c -o stirlerr.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dhyper.c -o dhyper.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_snps.o -c profile_snps.cpp consolidate.cpp:497:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 497 | char alts[no_alleles]; | ^~~~~~~~~~ consolidate.cpp:497:23: note: read of non-const variable 'no_alleles' is not allowed in a constant expression consolidate.cpp:494:21: note: declared here 494 | int32_t no_alleles = vs.size(); | ^ consolidate.cpp:734:27: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 734 | char alts[no_alleles]; | ^~~~~~~~~~ consolidate.cpp:734:27: note: read of non-const variable 'no_alleles' is not allowed in a constant expression consolidate.cpp:731:25: note: declared here 731 | int32_t no_alleles = vs.size(); | ^ 2 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o profile_vntrs.o -c profile_vntrs.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gamma.c -o gamma.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o program.o -c program.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c plnorm.c -o plnorm.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o read_filter.o -c read_filter.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o reference_sequence.o -c reference_sequence.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qgamma.c -o qgamma.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o rfhmm.o -c rfhmm.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o rfhmm_x.o -c rfhmm_x.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rexp.c -o rexp.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o rminfo.o -c rminfo.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c toms708.c -o toms708.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dlnorm.c -o dlnorm.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o seq.o -c seq.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gamma_cody.c -o gamma_cody.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c plogis.c -o plogis.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o set_ref.o -c set_ref.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o snp_genotyping_record.o -c snp_genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o sort.o -c sort.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qgeom.c -o qgeom.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rf.c -o rf.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c wilcox.c -o wilcox.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o subset.o -c subset.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o sv_tree.o -c sv_tree.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o svm_train.o -c svm_train.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c dlogis.c -o dlogis.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o svm_predict.o -c svm_predict.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c gammalims.c -o gammalims.o estimate.cpp:391:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 391 | int32_t g[ploidy]; | ^~~~~~ estimate.cpp:391:31: note: read of non-const variable 'ploidy' is not allowed in a constant expression estimate.cpp:344:21: note: declared here 344 | int32_t ploidy = bcf_get_genotypes(odr->hdr, v, >s, &n_gts); | ^ estimate.cpp:393:32: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 393 | int32_t AC[no_alleles]; | ^~~~~~~~~~ estimate.cpp:393:32: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:394:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 394 | float AF[no_alleles]; | ^~~~~~~~~~ estimate.cpp:394:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:399:32: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 399 | int32_t GC[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:399:32: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimate.cpp:401:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 401 | float GF[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:401:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimate.cpp:423:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 423 | float MLE_HWE_AF[no_alleles]; | ^~~~~~~~~~ estimate.cpp:423:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:424:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 424 | float MLE_HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:424:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ estimate.cpp:444:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 444 | float MLE_AF[no_alleles]; | ^~~~~~~~~~ estimate.cpp:444:26: note: read of non-const variable 'no_alleles' is not allowed in a constant expression estimate.cpp:358:21: note: declared here 358 | int32_t no_alleles = bcf_get_n_allele(v); | ^ estimate.cpp:445:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 445 | float MLE_GF[no_genotypes]; | ^~~~~~~~~~~~ estimate.cpp:445:26: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression estimate.cpp:381:21: note: declared here 381 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 9 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o tbx_ordered_reader.o -c tbx_ordered_reader.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c pnbeta.c -o pnbeta.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c qhyper.c -o qhyper.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o test.o -c test.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c rgamma.c -o rgamma.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o trio.o -c trio.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o union_variants.o -c union_variants.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sunif.c -o sunif.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o uniq.o -c uniq.cpp fuzzy_partition.cpp:153:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 153 | bcf_hdr_sync(odr->hdr); | ^~~~~~~~~~~~ ~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o utils.o -c utils.cpp cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c sexp.c -o sexp.o cc -fPIC -DMATHLIB_STANDALONE -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=gnu99 -IRmath -DNDEBUG -c snorm.c -o snorm.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o validate.o -c validate.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o variant.o -c variant.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o variant_manip.o -c variant_manip.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o variant_filter.o -c variant_filter.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o view.o -c view.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr.o -c vntr.cpp info2tab.cpp:278:57: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 278 | fprintf(out, "%s\t%d", bcf_get_chrom(h, v), bcf_get_pos1(v)); | ~~ ^~~~~~~~~~~~~~~ | %ld ./hts_utils.h:464:25: note: expanded from macro 'bcf_get_pos1' 464 | #define bcf_get_pos1(v) ((v)->pos+1) | ^~~~~~~~~~~~ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_annotator.o -c vntr_annotator.cpp ordered_bcf_overlap_matcher.cpp:34:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 34 | bcf_hdr_sync(odr->hdr); | ^~~~~~~~~~~~ ~~~~~~~~ ordered_bcf_overlap_matcher.cpp:52:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 52 | bcf_hdr_sync(odr->hdr); | ^~~~~~~~~~~~ ~~~~~~~~ 2 warnings generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_consolidator.o -c vntr_consolidator.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_extractor.o -c vntr_extractor.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_genotyping_record.o -c vntr_genotyping_record.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntr_tree.o -c vntr_tree.cpp rm -rf libRmath.a c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vntrize.o -c vntrize.cpp c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o wdp_ahmm.o -c wdp_ahmm.cpp ar -rc libRmath.a bd0.o dnbeta.o i1mach.o pnbinom.o qlnorm.o rgeom.o bessel_i.o dnbinom.o imax2.o pnchisq.o qlogis.o rhyper.o bessel_j.o dnchisq.o imin2.o pnf.o qnbeta.o rlnorm.o bessel_k.o dnf.o lbeta.o pnorm.o qnbinom.o rlogis.o bessel_y.o dnorm.o lgamma.o pnt.o qnchisq.o rmultinom.o beta.o dnt.o lgammacor.o polygamma.o qnf.o rnbinom.o chebyshev.o dpois.o log1p.o ppois.o qnorm.o rnchisq.o choose.o dt.o mlutils.o pt.o qnt.o rnorm.o d1mach.o dunif.o pbeta.o ptukey.o qpois.o rpois.o dbeta.o dweibull.o pbinom.o punif.o qt.o rt.o dbinom.o expm1.o pcauchy.o pweibull.o qtukey.o runif.o dcauchy.o fmax2.o pchisq.o qbeta.o qunif.o rweibull.o dchisq.o fmin2.o pexp.o qbinom.o qweibull.o dexp.o fprec.o pf.o qcauchy.o rbeta.o sign.o df.o fround.o pgamma.o qchisq.o rbinom.o signrank.o dgamma.o fsign.o pgeom.o qexp.o rcauchy.o dgeom.o ftrunc.o phyper.o qf.o rchisq.o stirlerr.o dhyper.o gamma.o plnorm.o qgamma.o rexp.o toms708.o dlnorm.o gamma_cody.o plogis.o qgeom.o rf.o wilcox.o dlogis.o gammalims.o pnbeta.o qhyper.o rgamma.o sunif.o sexp.o snorm.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o main.o -c main.cpp gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vt/work/vt-0.57721/lib/Rmath' merge_genotypes.cpp:215:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 215 | bcf_hdr_sync(odw->hdr); | ^~~~~~~~~~~~ ~~~~~~~~ 1 warning generated. compute_features2.cpp:219:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 219 | int32_t g[ploidy]; | ^~~~~~ compute_features2.cpp:219:23: note: read of non-const variable 'ploidy' is not allowed in a constant expression compute_features2.cpp:195:21: note: declared here 195 | int32_t ploidy = bcf_get_genotypes(odr->hdr, v, >s, &n_gts); | ^ compute_features2.cpp:221:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 221 | int32_t AC[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:221:24: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:222:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 222 | float AF[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:222:22: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:227:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 227 | int32_t GC[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:227:24: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features2.cpp:229:22: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 229 | float GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:229:22: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features2.cpp:249:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 249 | float MLE_HWE_AF[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:249:30: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:250:30: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 250 | float MLE_HWE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:250:30: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ compute_features2.cpp:260:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 260 | float MLE_AF[no_alleles]; | ^~~~~~~~~~ compute_features2.cpp:260:26: note: read of non-const variable 'no_alleles' is not allowed in a constant expression compute_features2.cpp:204:21: note: declared here 204 | int32_t no_alleles = bcf_get_n_allele(v); | ^ compute_features2.cpp:261:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 261 | float MLE_GF[no_genotypes]; | ^~~~~~~~~~~~ compute_features2.cpp:261:26: note: read of non-const variable 'no_genotypes' is not allowed in a constant expression compute_features2.cpp:226:21: note: declared here 226 | int32_t no_genotypes = bcf_an2gn(no_alleles); | ^ 9 warnings generated. profile_chm1.cpp:295:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 295 | int32_t na12878_index[no_overlap_files]; | ^~~~~~~~~~~~~~~~ profile_chm1.cpp:295:31: note: read of non-const variable 'no_overlap_files' is not allowed in a constant expression profile_chm1.cpp:285:17: note: declared here 285 | int32_t no_overlap_files = input_vcf_files.size(); | ^ 1 warning generated. paste.cpp:166:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 166 | bcf1_t* vs[nfiles]; | ^~~~~~ paste.cpp:166:20: note: read of non-const variable 'nfiles' is not allowed in a constant expression paste.cpp:137:17: note: declared here 137 | int32_t nfiles = odrs.size(); | ^ paste.cpp:194:37: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 194 | int32_t nval_per_sample[vs[0]->n_fmt]; | ^~~~~~~~~~~~ paste.cpp:194:37: note: read of non-constexpr variable 'vs' is not allowed in a constant expression paste.cpp:166:17: note: declared here 166 | bcf1_t* vs[nfiles]; | ^ paste.cpp:195:26: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 195 | int32_t size[vs[0]->n_fmt]; | ^~~~~~~~~~~~ paste.cpp:195:26: note: read of non-constexpr variable 'vs' is not allowed in a constant expression paste.cpp:166:17: note: declared here 166 | bcf1_t* vs[nfiles]; | ^ 3 warnings generated. sort.cpp:213:28: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 213 | bcf1_t *buffer[buffer_size]; | ^~~~~~~~~~~ sort.cpp:213:28: note: read of non-const variable 'buffer_size' is not allowed in a constant expression sort.cpp:211:20: note: declared here 211 | size_t buffer_size = 1000000; | ^ 1 warning generated. paste_genotypes.cpp:617:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 617 | const char* tmp_d_alleles[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:617:44: note: read of non-const variable 'k' is not allowed in a constant expression 617 | const char* tmp_d_alleles[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:623:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 623 | int tmp_filts[v_filts[k].size()]; | ^~~~~~~~~~~~~~~~~ paste_genotypes.cpp:623:31: note: read of non-const variable 'k' is not allowed in a constant expression 623 | int tmp_filts[v_filts[k].size()]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:633:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 633 | float MLE_HWE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:633:35: note: read of non-const variable 'k' is not allowed in a constant expression 633 | float MLE_HWE_AF[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:634:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 634 | float MLE_HWE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_genotypes.cpp:634:33: note: read of non-const variable 'k' is not allowed in a constant expression 634 | float MLE_HWE_GF[vn_genos[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:645:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 645 | int32_t acs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:645:30: note: read of non-const variable 'k' is not allowed in a constant expression 645 | int32_t acs[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:646:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 646 | int32_t gcs[vn_genos[k]]; | ^~~~~~~~~~~ paste_genotypes.cpp:646:28: note: read of non-const variable 'k' is not allowed in a constant expression 646 | int32_t gcs[vn_genos[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:647:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 647 | float afs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:647:28: note: read of non-const variable 'k' is not allowed in a constant expression 647 | float afs[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:713:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 713 | float MLE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_genotypes.cpp:713:31: note: read of non-const variable 'k' is not allowed in a constant expression 713 | float MLE_AF[vn_alleles[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_genotypes.cpp:714:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 714 | float MLE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_genotypes.cpp:714:29: note: read of non-const variable 'k' is not allowed in a constant expression 714 | float MLE_GF[vn_genos[k]]; | ^ paste_genotypes.cpp:609:16: note: declared here 609 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ 9 warnings generated. profile_mendelian.cpp:191:13: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] 191 | bcf_hdr_sync(odw->hdr); | ^~~~~~~~~~~~ ~~~~~~~~ 1 warning generated. milk_filter.cpp:456:96: warning: format specifies type 'int' but the argument has type 'hts_pos_t' (aka 'long') [-Wformat] 456 | fprintf(stderr,"Processing %d variants at %s:%d\n", nread + 1, bcf_seqname(odw->hdr,nv), nv->pos); | ~~ ^~~~~~~ | %ld 1 warning generated. subset.cpp:188:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 188 | int32_t g[ploidy]; | ^~~~~~ subset.cpp:188:23: note: read of non-const variable 'ploidy' is not allowed in a constant expression subset.cpp:185:21: note: declared here 185 | int32_t ploidy = bcf_get_genotypes(odw->hdr, v, >s, &n)/no_subset_samples; | ^ subset.cpp:190:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 190 | int32_t AC[n_allele]; | ^~~~~~~~ subset.cpp:190:24: note: read of non-const variable 'n_allele' is not allowed in a constant expression subset.cpp:186:21: note: declared here 186 | int32_t n_allele = bcf_get_n_allele(v); | ^ 2 warnings generated. paste_and_compute_features_sequential.cpp:589:33: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 589 | const char* tmp_d_alleles[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:589:44: note: read of non-const variable 'k' is not allowed in a constant expression 589 | const char* tmp_d_alleles[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:595:23: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 595 | int tmp_filts[v_filts[k].size()]; | ^~~~~~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:595:31: note: read of non-const variable 'k' is not allowed in a constant expression 595 | int tmp_filts[v_filts[k].size()]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:605:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 605 | float MLE_HWE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:605:35: note: read of non-const variable 'k' is not allowed in a constant expression 605 | float MLE_HWE_AF[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:606:24: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 606 | float MLE_HWE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_and_compute_features_sequential.cpp:606:33: note: read of non-const variable 'k' is not allowed in a constant expression 606 | float MLE_HWE_GF[vn_genos[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:617:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 617 | int32_t acs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:617:30: note: read of non-const variable 'k' is not allowed in a constant expression 617 | int32_t acs[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:618:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 618 | int32_t gcs[vn_genos[k]]; | ^~~~~~~~~~~ paste_and_compute_features_sequential.cpp:618:28: note: read of non-const variable 'k' is not allowed in a constant expression 618 | int32_t gcs[vn_genos[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:619:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 619 | float afs[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:619:28: note: read of non-const variable 'k' is not allowed in a constant expression 619 | float afs[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:685:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 685 | float MLE_AF[vn_alleles[k]]; | ^~~~~~~~~~~~~ paste_and_compute_features_sequential.cpp:685:31: note: read of non-const variable 'k' is not allowed in a constant expression 685 | float MLE_AF[vn_alleles[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ paste_and_compute_features_sequential.cpp:686:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 686 | float MLE_GF[vn_genos[k]]; | ^~~~~~~~~~~ paste_and_compute_features_sequential.cpp:686:29: note: read of non-const variable 'k' is not allowed in a constant expression 686 | float MLE_GF[vn_genos[k]]; | ^ paste_and_compute_features_sequential.cpp:582:16: note: declared here 582 | for(size_t k=0; k < v_rids.size(); ++k) { | ^ 9 warnings generated. profile_na12878.cpp:380:31: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 380 | int32_t na12878_index[no_overlap_files]; | ^~~~~~~~~~~~~~~~ profile_na12878.cpp:380:31: note: read of non-const variable 'no_overlap_files' is not allowed in a constant expression profile_na12878.cpp:369:17: note: declared here 369 | int32_t no_overlap_files = input_vcf_files.size(); | ^ 1 warning generated. c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I/usr/local/include -D__STDC_LIMIT_MACROS -o vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o -L/usr/local/lib -lhts lib/Rmath/libRmath.a lib/pcre2/libpcre2.a -ldeflate -lz -lpthread -lbz2 -llzma -lcurl -lcrypto =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for vt-0.57721_3 ===> Generating temporary packing list install -s -m 555 /wrkdirs/usr/ports/biology/vt/work/vt-0.57721/vt /wrkdirs/usr/ports/biology/vt/work/stage/usr/local/bin ====> 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=2025-11-09T23:29:54+0000' 'PKG_NOTE_ports_top_git_hash=ec159283c191' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=173b9df467e9' '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 vt-0.57721_3 ===> Building vt-0.57721_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for vt-0.57721_3 build of biology/vt | vt-0.57721_3 ended at Sun Nov 9 18:30:52 EST 2025 build time: 00:00:59