Date: Thu, 20 Aug 2020 05:14:18 GMT From: pkg-fallout@FreeBSD.org To: jwb@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-i386-default][biology/vcftools] Failed for vcftools-0.1.16 in build Message-ID: <202008200514.07K5EIZx011150@beefy17.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/vcftools/Makefile 476330 2018-08-04 01:29:29Z jwb $ Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p545479_s364329/logs/vcftools-0.1.16.log Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p545479_s364329 Log: =>> Building biology/vcftools build started at Thu Aug 20 05:13:17 UTC 2020 port directory: /usr/ports/biology/vcftools package name: vcftools-0.1.16 building for: FreeBSD head-i386-default-job-09 13.0-CURRENT FreeBSD 13.0-CURRENT 1300109 i386 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/vcftools/Makefile 476330 2018-08-04 01:29:29Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300109 Job Id: 09 !!! Jail is newer than host. (Jail: 1300109, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1300109 UNAME_v=FreeBSD 13.0-CURRENT 1300109 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root 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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-i386-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-- jwb@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 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 SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work 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 NO_PIE=yes 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=" -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" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.0 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 MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /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 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300109 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) 524288 stack size (kbytes, -s) 65536 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-1.14.7.txz [head-i386-default-job-09] Installing pkg-1.14.7... [head-i386-default-job-09] Extracting pkg-1.14.7: .......... 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.txz [head-i386-default-job-09] Installing gmake-4.3_2... [head-i386-default-job-09] `-- Installing gettext-runtime-0.21... [head-i386-default-job-09] | `-- Installing indexinfo-0.3.1... [head-i386-default-job-09] | `-- Extracting indexinfo-0.3.1: .... done [head-i386-default-job-09] `-- Extracting gettext-runtime-0.21: .......... done <snip> 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 thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking whether gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking 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 grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for 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 stdbool.h that conforms to C99... (cached) yes checking for _Bool... (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 for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for 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_setters.Tpo .deps/vcftools-entry_setters.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-entry_filters.Tpo .deps/vcftools-entry_filters.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-gamma.Tpo .deps/vcftools-gamma.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: warning: 'random_shuffle<std::__1::__wrap_iter<unsigned int *>>' is deprecated [-Wdeprecated-declarations] random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order ^ /usr/include/c++/v1/algorithm:3095:1: note: 'random_shuffle<std::__1::__wrap_iter<unsigned int *>>' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX14 void ^ /usr/include/c++/v1/__config:991:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED ^ /usr/include/c++/v1/__config:974:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 1 warning generated. mv -f .deps/vcftools-variant_file_filters.Tpo .deps/vcftools-variant_file_filters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file_format_convert.o -MD -MP -MF .deps/vcftools-variant_file_format_convert.Tpo -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file_output.o -MD -MP -MF .deps/vcftools-variant_file_output.Tpo -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp mv -f .deps/vcftools-variant_file_format_convert.Tpo .deps/vcftools-variant_file_format_convert.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-vcf_entry.o -MD -MP -MF .deps/vcftools-vcf_entry.Tpo -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp mv -f .deps/vcftools-vcf_entry.Tpo .deps/vcftools-vcf_entry.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-vcf_entry_setters.o -MD -MP -MF .deps/vcftools-vcf_entry_setters.Tpo -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp mv -f .deps/vcftools-vcf_entry_setters.Tpo .deps/vcftools-vcf_entry_setters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-vcf_file.o -MD -MP -MF .deps/vcftools-vcf_file.Tpo -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp mv -f .deps/vcftools-vcf_file.Tpo .deps/vcftools-vcf_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-vcftools.o -MD -MP -MF .deps/vcftools-vcftools.Tpo -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp mv -f .deps/vcftools-variant_file_output.Tpo .deps/vcftools-variant_file_output.Po mv -f .deps/vcftools-vcftools.Tpo .deps/vcftools-vcftools.Po c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz ld: error: undefined symbol: std::__1::__rs_get() >>> referenced by variant_file_filters.cpp >>> vcftools-variant_file_filters.o:(void std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned int*>)) ld: error: undefined symbol: std::__1::__rs_default::operator()() >>> referenced by variant_file_filters.cpp >>> vcftools-variant_file_filters.o:(void std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned int*>)) >>> referenced by variant_file_filters.cpp >>> vcftools-variant_file_filters.o:(void std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned int*>)) ld: error: undefined symbol: std::__1::__rs_default::~__rs_default() >>> referenced by variant_file_filters.cpp >>> vcftools-variant_file_filters.o:(void std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned int*>)) >>> referenced by variant_file_filters.cpp >>> vcftools-variant_file_filters.o:(void std::__1::random_shuffle<std::__1::__wrap_iter<unsigned int*> >(std::__1::__wrap_iter<unsigned int*>, std::__1::__wrap_iter<unsigned int*>)) c++: error: linker command failed with exit code 1 (use -v to see invocation) gmake[4]: *** [Makefile:465: vcftools] Error 1 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp' gmake[3]: *** [Makefile:319: all-recursive] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src' gmake[2]: *** [Makefile:362: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16' gmake[1]: *** [Makefile:303: 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
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