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Maintainer: j...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p8fb94260154e_s510fd83138/logs/vcftools-0.1.16.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building biology/vcftools build started at Sat Jul 15 05:51:27 UTC 2023 port directory: /usr/ports/biology/vcftools package name: vcftools-0.1.16 building for: FreeBSD main-arm64-default-job-04 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm64 maintained by: j...@freebsd.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400093 Job Id: 04 !!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400093 UNAME_v=FreeBSD 14.0-CURRENT 1400093 UNAME_r=14.0-CURRENT 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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- j...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcftools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.71 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/vcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/vcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/vcftools/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 DEFAULT_AUTOCONF=2.71 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" B SD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/vcftools" EXAMPLESDIR="share/examples/vcftools" DATADIR="share/vcftools" WWWDIR="www/vcftools" ETCDIR="etc/vcftools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcftools DOCSDIR=/usr/local/share/doc/vcftools EXAMPLESDIR=/usr/local/share/examples/vcftools WWWDIR=/usr/local/www/vcftools ETCDIR=/usr/local/etc/vcftools --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400093 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License LGPL3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [main-arm64-default-job-04] Installing pkg-1.20.4... [main-arm64-default-job-04] Extracting pkg-1.20.4: .......... done ===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of vcftools-0.1.16 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.16 for building =========================================================================== =======================<phase: checksum >============================ ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.16 for building => SHA256 Checksum OK for vcftools-vcftools-v0.1.16_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by vcftools-0.1.16 for building ===> Extracting for vcftools-0.1.16 => SHA256 Checksum OK for vcftools-vcftools-v0.1.16_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for vcftools-0.1.16 =========================================================================== =======================<phase: build-depends >============================ ===> vcftools-0.1.16 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-arm64-default-job-04] Installing gmake-4.3_2... [main-arm64-default-job-04] `-- Installing gettext-runtime-0.22... [main-arm64-default-job-04] | `-- Installing indexinfo-0.3.1... [main-arm64-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done [main-arm64-default-job-04] `-- Extracting gettext-runtime-0.22: .......... done [main-arm64-default-job-04] Extracting gmake-4.3_2: .......... done ===> vcftools-0.1.16 depends on package: gmake>=4.3 - found ===> Returning to build of vcftools-0.1.16 ===> vcftools-0.1.16 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.8.1,1.pkg [main-arm64-default-job-04] Installing pkgconf-1.8.1,1... [main-arm64-default-job-04] Extracting pkgconf-1.8.1,1: .......... done ===> vcftools-0.1.16 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of vcftools-0.1.16 ===> vcftools-0.1.16 depends on package: autoconf>=2.71 - not found ===> Installing existing package /packages/All/autoconf-2.71.pkg [main-arm64-default-job-04] Installing autoconf-2.71... [main-arm64-default-job-04] `-- Installing autoconf-switch-20220527... [main-arm64-default-job-04] `-- Extracting autoconf-switch-20220527: .......... done [main-arm64-default-job-04] `-- Installing m4-1.4.19,1... [main-arm64-default-job-04] `-- Extracting m4-1.4.19,1: .......... done [main-arm64-default-job-04] `-- Installing perl5-5.32.1_4... [main-arm64-default-job-04] `-- Extracting perl5-5.32.1_4: .......... done [main-arm64-default-job-04] Extracting autoconf-2.71: .......... done ===> vcftools-0.1.16 depends on package: autoconf>=2.71 - found ===> Returning to build of vcftools-0.1.16 ===> vcftools-0.1.16 depends on package: automake>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5.pkg [main-arm64-default-job-04] Installing automake-1.16.5... [main-arm64-default-job-04] Extracting automake-1.16.5: .......... done ===> vcftools-0.1.16 depends on package: automake>=1.16.5 - found ===> Returning to build of vcftools-0.1.16 ===> vcftools-0.1.16 depends on package: perl5>=5.32.r0<5.33 - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for vcftools-0.1.16 configure.ac:16: installing './compile' configure.ac:66: installing './config.guess' configure.ac:66: installing './config.sub' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './depcomp' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking for perl... (cached) /usr/local/bin/perl checking pkg-config is at least version 0.9.0... yes checking for ZLIB... yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for arpa/inet.h... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for netdb.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for inline... inline checking for int16_t... (cached) yes checking for int32_t... (cached) yes checking for int64_t... (cached) yes checking for int8_t... (cached) yes checking for off_t... (cached) yes checking for size_t... (cached) yes checking for ssize_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint8_t... (cached) yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for error_at_line... no checking build system type... aarch64-portbld-freebsd14.0 checking host system type... aarch64-portbld-freebsd14.0 checking for GNU libc compatible malloc... (cached) yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... (cached) yes checking for memset... (cached) yes checking for pow... no checking for select... (cached) yes checking for socket... yes checking for sqrt... no checking for strchr... (cached) yes checking for strdup... (cached) yes checking for strerror... (cached) yes checking for strstr... (cached) yes checking for strtol... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =======================<phase: build >============================ ===> Building for vcftools-0.1.16 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' gmake all-recursive gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' Making all in src gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' Making all in cpp gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp' c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bcf_entry.o -MD -MP -MF .deps/vcftools-bcf_entry.Tpo -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bcf_entry_setters.o -MD -MP -MF .deps/vcftools-bcf_entry_setters.Tpo -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp bcf_entry_setters.cpp:309:13: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion] if (tmp == 0x7F800001) ~~ ^~~~~~~~~~ bcf_entry_setters.cpp:326:28: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion] if ( (in == -1) or (in == 0x7F800001) ) ~~ ^~~~~~~~~~ 2 warnings generated. mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bcf_file.o -MD -MP -MF .deps/vcftools-bcf_file.Tpo -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bgzf.o -MD -MP -MF .deps/vcftools-bgzf.Tpo -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c mv -f .deps/vcftools-bgzf.Tpo .deps/vcftools-bgzf.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp mv -f .deps/vcftools-dgeev.Tpo .deps/vcftools-dgeev.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp entry.cpp:601:12: warning: implicit conversion from 'int' to 'float' changes value from 2139095042 to 2139095040 [-Wimplicit-const-int-float-conversion] value = 0x7F800002; ~ ^~~~~~~~~~ mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry_filters.o -MD -MP -MF .deps/vcftools-entry_filters.Tpo -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp 1 warning generated. mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry_getters.o -MD -MP -MF .deps/vcftools-entry_getters.Tpo -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry_setters.o -MD -MP -MF .deps/vcftools-entry_setters.Tpo -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-gamma.o -MD -MP -MF .deps/vcftools-gamma.Tpo -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp mv -f .deps/vcftools-gamma.Tpo .deps/vcftools-gamma.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-knetfile.o -MD -MP -MF .deps/vcftools-knetfile.Tpo -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-output_log.o -MD -MP -MF .deps/vcftools-output_log.Tpo -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp mv -f .deps/vcftools-output_log.Tpo .deps/vcftools-output_log.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file.o -MD -MP -MF .deps/vcftools-variant_file.Tpo -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp mv -f .deps/vcftools-variant_file.Tpo .deps/vcftools-variant_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file_diff.o -MD -MP -MF .deps/vcftools-variant_file_diff.Tpo -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file_filters.o -MD -MP -MF .deps/vcftools-variant_file_filters.Tpo -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp variant_file_filters.cpp:129:2: error: use of undeclared identifier 'random_shuffle' random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order ^ 1 error generated. gmake[4]: *** [Makefile:766: vcftools-variant_file_filters.o] Error 1 gmake[4]: *** Waiting for unfinished jobs.... mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp' gmake[3]: *** [Makefile:329: all-recursive] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[2]: *** [Makefile:374: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' gmake[1]: *** [Makefile:315: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/vcftools
