build started at Thu Jul 9 18:59:03 CEST 2020 port directory: /usr/ports/biology/treekin package name: treekin-0.5.1_2 building for: FreeBSD 13amd64-default 13.0-CURRENT FreeBSD 13.0-CURRENT 1300098 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/treekin/Makefile 524642 2020-01-30 14:17:44Z swills $ Poudriere version: 3.3.4 Host OSVERSION: 1300098 Jail OSVERSION: 1300098 Job Id: ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300098 UNAME_v=FreeBSD 13.0-CURRENT 1300098 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 TRYBROKEN=yes LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.3.4 MASTERMNT=/usr/local/poudriere/data/.m/13amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=xterm-256color PWD=/usr/local/poudriere/data/.m/13amd64-default/ref/.p NO_WARNING_PKG_INSTALL_EOL=yes P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=13amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/13amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/testport.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV=PACKAGES=/tmp/pkgs PKGREPOSITORY=/tmp/pkgs PKGLATESTREPOSITORY=/tmp/pkgs/Latest FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran9" FC="gfortran9" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc9" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc9" MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/treekin/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/treekin/work HOME=/wrkdirs/usr/ports/biology/treekin/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/treekin/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran9" FC="gfortran9" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc9" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/treekin/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/treekin/work HOME=/wrkdirs/usr/ports/biology/treekin/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/treekin/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 -B/usr/local/bin -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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 DOCSDIR="share/doc/treekin" EXAMPLESDIR="share/examples/treekin" DATADIR="share/treekin" WWWDIR="www/treekin" ETCDIR="etc/treekin" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/treekin DOCSDIR=/usr/local/share/doc/treekin EXAMPLESDIR=/usr/local/share/examples/treekin WWWDIR=/usr/local/www/treekin ETCDIR=/usr/local/etc/treekin --End SUB_LIST-- ---Begin make.conf--- 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 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-rc1-0-gf79cd71e145) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-rc1-0-gf79cd71e145) Target: x86_64-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" "-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 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-rc1-0-gf79cd71e145) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300098 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES _SMP_CPUS=8 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) 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) 19400 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-- =================================================== ===> License LatticeLib accepted by the user =========================================================================== =================================================== ===> treekin-0.5.1_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.6.txz [13amd64-default] Installing pkg-1.14.6... [13amd64-default] Extracting pkg-1.14.6: .......... done ===> treekin-0.5.1_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of treekin-0.5.1_2 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LatticeLib accepted by the user ===> treekin-0.5.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by treekin-0.5.1_2 for building =========================================================================== =================================================== ===> License LatticeLib accepted by the user ===> treekin-0.5.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by treekin-0.5.1_2 for building => SHA256 Checksum OK for Treekin-0.5.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License LatticeLib accepted by the user ===> treekin-0.5.1_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by treekin-0.5.1_2 for building ===> Extracting for treekin-0.5.1_2 => SHA256 Checksum OK for Treekin-0.5.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for treekin-0.5.1_2 =========================================================================== =================================================== ===> treekin-0.5.1_2 depends on package: lapacke>0 - not found ===> Installing existing package /packages/All/lapacke-3.9.0.txz [13amd64-default] Installing lapacke-3.9.0... [13amd64-default] `-- Installing blas-3.9.0... [13amd64-default] | `-- Installing gcc9-9.3.0_1... [13amd64-default] | | `-- Installing binutils-2.33.1_2,1... [13amd64-default] | | `-- Installing gettext-runtime-0.20.2... [13amd64-default] | | | `-- Installing indexinfo-0.3.1... [13amd64-default] | | | `-- Extracting indexinfo-0.3.1: .... done [13amd64-default] | | `-- Extracting gettext-runtime-0.20.2: .......... done [13amd64-default] | | `-- Extracting binutils-2.33.1_2,1: .......... done [13amd64-default] | | `-- Installing gmp-6.2.0... [13amd64-default] | | `-- Extracting gmp-6.2.0: .......... done [13amd64-default] | | `-- Installing mpc-1.1.0_2... [13amd64-default] | | `-- Installing mpfr-4.0.2... [13amd64-default] | | `-- Extracting mpfr-4.0.2: .......... done [13amd64-default] | | `-- Extracting mpc-1.1.0_2: ......... done [13amd64-default] | `-- Extracting gcc9-9.3.0_1: .......... done [13amd64-default] `-- Extracting blas-3.9.0: ........ done [13amd64-default] `-- Installing lapack-3.9.0... [13amd64-default] `-- Extracting lapack-3.9.0: .......... done [13amd64-default] Extracting lapacke-3.9.0: .......... done ===== Message from gcc9-9.3.0_1: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc9 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> treekin-0.5.1_2 depends on package: lapacke>0 - found ===> Returning to build of treekin-0.5.1_2 ===> treekin-0.5.1_2 depends on executable: gfortran9 - found ===> treekin-0.5.1_2 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [13amd64-default] Installing gmake-4.3_2... [13amd64-default] Extracting gmake-4.3_2: .......... done ===> treekin-0.5.1_2 depends on package: gmake>=4.3 - found ===> Returning to build of treekin-0.5.1_2 ===> treekin-0.5.1_2 depends on file: /usr/local/bin/as - found ===> treekin-0.5.1_2 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.1_1.txz [13amd64-default] Installing ccache-3.7.1_1... [13amd64-default] Extracting ccache-3.7.1_1: .......... 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 gcc9 create symlink for gcc9 (world) create symlink for g++9 create symlink for g++9 (world) create symlink for cpp9 create symlink for cpp9 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.1_1: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> treekin-0.5.1_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of treekin-0.5.1_2 =========================================================================== =================================================== ===> treekin-0.5.1_2 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> treekin-0.5.1_2 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) =========================================================================== =>> Recording filesystem state for prebuild... done =================================================== ===> treekin-0.5.1_2 depends on package: lapacke>0 - found ===> treekin-0.5.1_2 depends on executable: gfortran9 - found ===> treekin-0.5.1_2 depends on package: gmake>=4.3 - found ===> treekin-0.5.1_2 depends on file: /usr/local/bin/as - found ===> treekin-0.5.1_2 depends on file: /usr/local/bin/ccache - found ===> treekin-0.5.1_2 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> treekin-0.5.1_2 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Configuring for treekin-0.5.1_2 configure: loading site script /usr/ports/Templates/config.site checking whether gmake supports nested variables... yes 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 build system type... amd64-portbld-freebsd13.0 checking host system type... amd64-portbld-freebsd13.0 checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for style of include used by gmake... GNU checking dependency style of c++... gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for ranlib... /usr/local/bin/ranlib checking whether gmake sets $(MAKE)... (cached) yes checking for autoconf... autoconf checking for aclocal... aclocal checking for make... /wrkdirs/usr/ports/biology/treekin/work/.bin/make checking for ar... /usr/local/bin/ar checking whether c++ supports C++11 features with -std=gnu++11... yes checking for gengetopt... no checking for sgemm_... no checking for ATL_xerbla in -latlas... no checking for sgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for sgemm_ in -lmkl... no checking for sgemm_... (cached) no checking for sgemm_ in -lcxml... no checking for sgemm_ in -ldxml... no checking for sgemm_ in -lscs... no checking for sgemm_ in -lcomplib.sgimath... no checking for sgemm_ in -lblas... (cached) yes checking for sgemm_ in -lessl... no checking for sgemm_ in -lblas... (cached) yes checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran9 accepts -g... yes checking how to get verbose linking output from gfortran9... -v checking for Fortran 77 libraries of gfortran9... -L/usr/local/lib -L/usr/local/lib/gcc9 -L/usr/local/bin -L/usr/local/lib/gcc9/gcc/x86_64-portbld-freebsd13.0/9.3.0 -L/usr/local/lib/gcc9/gcc/x86_64-portbld-freebsd13.0/9.3.0/../../../../../x86_64-portbld-freebsd13.0/lib -L/usr/local/lib/gcc9/gcc/x86_64-portbld-freebsd13.0/9.3.0/../../.. -lgfortran -lm -lssp_nonshared -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for cheev_... no checking for cheev_ in -llapack... yes checking openblas/lapacke.h usability... no checking openblas/lapacke.h presence... no checking for openblas/lapacke.h... no checking lapacke/lapacke.h usability... yes checking lapacke/lapacke.h presence... yes checking for lapacke/lapacke.h... yes checking for ANSI C header files... (cached) yes checking for errno.h... (cached) yes checking for math.h... (cached) yes checking for pkg-config... no checking how to run the C++ preprocessor... c++ -std=gnu++11 -E checking for mlapack... no configure: WARNING: ********************************************************************** Failed to setup linking the program against the MLAPACK library. In case you have installed mlapack in a non-standard directory, consider using the --with-mlapack=/path/to/mlapack parameter to specify the location where to find MLAPACK. Otherwise, you can obtain the mlapack library from https://github.com/RaumZeit/mlapack ********************************************************************** checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for help2man... no 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 packaging/treekin.spec config.status: creating packaging/PKGBUILD config.status: creating packaging/treekin-mlapack.spec config.status: creating packaging/PKGBUILD-mlapack config.status: creating man/Makefile config.status: creating man/cmdlopt.sh config.status: creating config.h config.status: executing depfiles commands configure: ====================================== Treekin 0.5.1 ====================================== Configured successful with the following options: Extra Libraries --------------- * MLapack : no ( mlapack library missing or not of version 0.8 or higher ) Install Directories ------------------- * Executables : /usr/local/bin * Libraries : /usr/local/lib * Header files : /usr/local/include * Extra Data : /usr/local/share * Man pages : /usr/local/man Note, that the most recent version of the DrTransformer program requires Treekin to be linked against the MLAPACK library! You can run make now. =========================================================================== =================================================== ===> Building for treekin-0.5.1_2 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' /wrkdirs/usr/ports/biology/treekin/work/.bin/make all-recursive make[2]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' Making all in src make[3]: Entering directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-mxccm.o -MD -MP -MF .deps/treekin-mxccm.Tpo -c -o treekin-mxccm.o `test -f 'mxccm.cpp' || echo './'`mxccm.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-globals.o -MD -MP -MF .deps/treekin-globals.Tpo -c -o treekin-globals.o `test -f 'globals.cpp' || echo './'`globals.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-barparser.o -MD -MP -MF .deps/treekin-barparser.Tpo -c -o treekin-barparser.o `test -f 'barparser.cpp' || echo './'`barparser.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-calcpp.o -MD -MP -MF .deps/treekin-calcpp.Tpo -c -o treekin-calcpp.o `test -f 'calcpp.cpp' || echo './'`calcpp.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-calc.o -MD -MP -MF .deps/treekin-calc.Tpo -c -o treekin-calc.o `test -f 'calc.cpp' || echo './'`calc.cpp c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-exp_matrix.o -MD -MP -MF .deps/treekin-exp_matrix.Tpo -c -o treekin-exp_matrix.o `test -f 'exp_matrix.cpp' || echo './'`exp_matrix.cpp cc -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT treekin-treekin_cmdline.o -MD -MP -MF .deps/treekin-treekin_cmdline.Tpo -c -o treekin-treekin_cmdline.o `test -f 'treekin_cmdline.c' || echo './'`treekin_cmdline.c c++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I.. -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treekin-main.o -MD -MP -MF .deps/treekin-main.Tpo -c -o treekin-main.o `test -f 'main.cpp' || echo './'`main.cpp mv -f .deps/treekin-treekin_cmdline.Tpo .deps/treekin-treekin_cmdline.Po mv -f .deps/treekin-mxccm.Tpo .deps/treekin-mxccm.Po mv -f .deps/treekin-globals.Tpo .deps/treekin-globals.Po mv -f .deps/treekin-barparser.Tpo .deps/treekin-barparser.Po mv -f .deps/treekin-exp_matrix.Tpo .deps/treekin-exp_matrix.Po In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:167:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:250:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:259:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:263:8: error: explicit specialization of undeclared template struct '__throw_with_nested' struct __throw_with_nested<_Tp, _Up, true> { ^ ~~~~~~~~~~~~~~~~ /usr/include/c++/v1/exception:262:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:272:8: error: explicit specialization of undeclared template struct '__throw_with_nested' struct __throw_with_nested<_Tp, _Up, false> { ^ ~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/exception:271:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:285:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:293:5: error: no template named '__throw_with_nested' __throw_with_nested<_Tp, _Up, ^ /usr/include/c++/v1/exception:304:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:314:39: error: no template named '__can_dynamic_cast' typename enable_if< __can_dynamic_cast<_Ep, nested_exception>::value>::type* = 0) ^ /usr/include/c++/v1/exception:314:90: error: parameter declarator cannot be qualified typename enable_if< __can_dynamic_cast<_Ep, nested_exception>::value>::type* = 0) ~~^ /usr/include/c++/v1/exception:314:94: error: expected ')' typename enable_if< __can_dynamic_cast<_Ep, nested_exception>::value>::type* = 0) ^ /usr/include/c++/v1/exception:313:18: note: to match this '(' rethrow_if_nested(const _Ep& __e, ^ /usr/include/c++/v1/exception:310:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:45: /usr/include/c++/v1/exception:325:39: error: no template named '__can_dynamic_cast' typename enable_if::value>::type* = 0) ^ /usr/include/c++/v1/exception:325:90: error: parameter declarator cannot be qualified typename enable_if::value>::type* = 0) ~~^ /usr/include/c++/v1/exception:325:94: error: expected ')' typename enable_if::value>::type* = 0) ^ /usr/include/c++/v1/exception:324:18: note: to match this '(' rethrow_if_nested(const _Ep&, ^ /usr/include/c++/v1/exception:321:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calcpp.cpp:6: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:244: In file included from /usr/include/c++/v1/stdexcept:46: /usr/include/c++/v1/iosfwd:105:1: error: templates must have C++ linkage template struct _LIBCPP_TEMPLATE_VIS char_traits; ^~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[3]: *** [Makefile:514: treekin-calcpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... In file included from calc.cpp:6: In file included from ./calc.h:30: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:246: In file included from /usr/include/c++/v1/sstream:173: In file included from /usr/include/c++/v1/ostream:138: In file included from /usr/include/c++/v1/ios:215: In file included from /usr/include/c++/v1/__locale:14: In file included from /usr/include/c++/v1/string:504: In file included from /usr/include/c++/v1/string_view:175: /usr/include/c++/v1/__string:75:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from calc.cpp:6: In file included from ./calc.h:30: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:246: In file included from /usr/include/c++/v1/sstream:173: In file included from /usr/include/c++/v1/ostream:138: In file included from /usr/include/c++/v1/ios:215: In file included from /usr/include/c++/v1/__locale:14: In file included from /usr/include/c++/v1/string:504: In file included from /usr/include/c++/v1/string_view:175: /usr/include/c++/v1/__string:120:36: error: unknown type name 'char_type' char_traits<_CharT>::compare(const char_type* __s1, const char_type* __s2, size_t __n) ^ /usr/include/c++/v1/__string:120:59: error: unknown type name 'char_type' char_traits<_CharT>::compare(const char_type* __s1, const char_type* __s2, size_t __n) ^ /usr/include/c++/v1/__string:120:22: error: out-of-line definition of 'compare' from class 'char_traits<_CharT>' without definition char_traits<_CharT>::compare(const char_type* __s1, const char_type* __s2, size_t __n) ~~~~~~~~~~~~~~~~~~~~~^ /usr/include/c++/v1/__string:122:12: error: use of undeclared identifier '__n'; did you mean '__1'? for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:71:1: note: '__1' declared here _LIBCPP_BEGIN_NAMESPACE_STD ^ /usr/include/c++/v1/__config:780:70: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD' #define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE { ^ /usr/include/c++/v1/__config:130:32: note: expanded from macro '_LIBCPP_ABI_NAMESPACE' # define _LIBCPP_ABI_NAMESPACE _LIBCPP_CONCAT(__,_LIBCPP_ABI_VERSION) ^ /usr/include/c++/v1/__config:127:45: note: expanded from macro '_LIBCPP_CONCAT' #define _LIBCPP_CONCAT(_LIBCPP_X,_LIBCPP_Y) _LIBCPP_CONCAT1(_LIBCPP_X,_LIBCPP_Y) ^ /usr/include/c++/v1/__config:126:46: note: expanded from macro '_LIBCPP_CONCAT1' #define _LIBCPP_CONCAT1(_LIBCPP_X,_LIBCPP_Y) _LIBCPP_X##_LIBCPP_Y ^ :570:1: note: expanded from here __1 ^ In file included from calc.cpp:6: In file included from ./calc.h:30: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:246: In file included from /usr/include/c++/v1/sstream:173: In file included from /usr/include/c++/v1/ostream:138: In file included from /usr/include/c++/v1/ios:215: In file included from /usr/include/c++/v1/__locale:14: In file included from /usr/include/c++/v1/string:504: In file included from /usr/include/c++/v1/string_view:175: /usr/include/c++/v1/__string:122:12: error: unexpected namespace name '__1': expected expression for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:122:19: error: use of undeclared identifier '__n' for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:122:26: error: use of undeclared identifier '__s1' for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:122:34: error: use of undeclared identifier '__s2' for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:124:17: error: use of undeclared identifier '__s1' if (lt(*__s1, *__s2)) ^ /usr/include/c++/v1/__string:124:24: error: use of undeclared identifier '__s2' if (lt(*__s1, *__s2)) ^ /usr/include/c++/v1/__string:126:17: error: use of undeclared identifier '__s2' if (lt(*__s2, *__s1)) ^ /usr/include/c++/v1/__string:126:24: error: use of undeclared identifier '__s1' if (lt(*__s2, *__s1)) ^ /usr/include/c++/v1/__string:135:35: error: unknown type name 'char_type' char_traits<_CharT>::length(const char_type* __s) ^ /usr/include/c++/v1/__string:135:22: error: out-of-line definition of 'length' from class 'char_traits<_CharT>' without definition char_traits<_CharT>::length(const char_type* __s) ~~~~~~~~~~~~~~~~~~~~~^ /usr/include/c++/v1/__string:138:22: error: use of undeclared identifier 'char_type' for (; !eq(*__s, char_type(0)); ++__s) ^ /usr/include/c++/v1/__string:138:17: error: use of undeclared identifier '__s' for (; !eq(*__s, char_type(0)); ++__s) ^ /usr/include/c++/v1/__string:138:39: error: use of undeclared identifier '__s' for (; !eq(*__s, char_type(0)); ++__s) ^ /usr/include/c++/v1/__string:146:33: error: unknown type name 'char_type' char_traits<_CharT>::find(const char_type* __s, size_t __n, const char_type& __a) ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[3]: *** [Makefile:528: treekin-calc.o] Error 1 In file included from main.cpp:16: In file included from ./calc.h:30: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:246: In file included from /usr/include/c++/v1/sstream:173: In file included from /usr/include/c++/v1/ostream:138: In file included from /usr/include/c++/v1/ios:215: In file included from /usr/include/c++/v1/__locale:14: In file included from /usr/include/c++/v1/string:504: In file included from /usr/include/c++/v1/string_view:175: /usr/include/c++/v1/__string:75:1: error: templates must have C++ linkage template ^~~~~~~~~~~~~~~~~~~~~~~ /usr/local/include/lapacke/lapack.h:16:1: note: extern "C" language linkage specification begins here extern "C" { ^ In file included from main.cpp:16: In file included from ./calc.h:30: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:246: In file included from /usr/include/c++/v1/sstream:173: In file included from /usr/include/c++/v1/ostream:138: In file included from /usr/include/c++/v1/ios:215: In file included from /usr/include/c++/v1/__locale:14: In file included from /usr/include/c++/v1/string:504: In file included from /usr/include/c++/v1/string_view:175: /usr/include/c++/v1/__string:120:36: error: unknown type name 'char_type' char_traits<_CharT>::compare(const char_type* __s1, const char_type* __s2, size_t __n) ^ /usr/include/c++/v1/__string:120:59: error: unknown type name 'char_type' char_traits<_CharT>::compare(const char_type* __s1, const char_type* __s2, size_t __n) ^ /usr/include/c++/v1/__string:120:22: error: out-of-line definition of 'compare' from class 'char_traits<_CharT>' without definition char_traits<_CharT>::compare(const char_type* __s1, const char_type* __s2, size_t __n) ~~~~~~~~~~~~~~~~~~~~~^ /usr/include/c++/v1/__string:122:12: error: use of undeclared identifier '__n'; did you mean '__1'? for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:71:1: note: '__1' declared here _LIBCPP_BEGIN_NAMESPACE_STD ^ /usr/include/c++/v1/__config:780:70: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD' #define _LIBCPP_BEGIN_NAMESPACE_STD namespace std { inline namespace _LIBCPP_ABI_NAMESPACE { ^ /usr/include/c++/v1/__config:130:32: note: expanded from macro '_LIBCPP_ABI_NAMESPACE' # define _LIBCPP_ABI_NAMESPACE _LIBCPP_CONCAT(__,_LIBCPP_ABI_VERSION) ^ /usr/include/c++/v1/__config:127:45: note: expanded from macro '_LIBCPP_CONCAT' #define _LIBCPP_CONCAT(_LIBCPP_X,_LIBCPP_Y) _LIBCPP_CONCAT1(_LIBCPP_X,_LIBCPP_Y) ^ /usr/include/c++/v1/__config:126:46: note: expanded from macro '_LIBCPP_CONCAT1' #define _LIBCPP_CONCAT1(_LIBCPP_X,_LIBCPP_Y) _LIBCPP_X##_LIBCPP_Y ^ :570:1: note: expanded from here __1 ^ In file included from main.cpp:16: In file included from ./calc.h:30: In file included from ./calcpp.h:52: In file included from /usr/local/include/lapacke/lapacke.h:37: In file included from /usr/local/include/lapacke/lapack.h:55: In file included from /usr/include/c++/v1/complex.h:28: In file included from /usr/include/c++/v1/ccomplex:20: In file included from /usr/include/c++/v1/complex:246: In file included from /usr/include/c++/v1/sstream:173: In file included from /usr/include/c++/v1/ostream:138: In file included from /usr/include/c++/v1/ios:215: In file included from /usr/include/c++/v1/__locale:14: In file included from /usr/include/c++/v1/string:504: In file included from /usr/include/c++/v1/string_view:175: /usr/include/c++/v1/__string:122:12: error: unexpected namespace name '__1': expected expression for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:122:19: error: use of undeclared identifier '__n' for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:122:26: error: use of undeclared identifier '__s1' for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:122:34: error: use of undeclared identifier '__s2' for (; __n; --__n, ++__s1, ++__s2) ^ /usr/include/c++/v1/__string:124:17: error: use of undeclared identifier '__s1' if (lt(*__s1, *__s2)) ^ /usr/include/c++/v1/__string:124:24: error: use of undeclared identifier '__s2' if (lt(*__s1, *__s2)) ^ /usr/include/c++/v1/__string:126:17: error: use of undeclared identifier '__s2' if (lt(*__s2, *__s1)) ^ /usr/include/c++/v1/__string:126:24: error: use of undeclared identifier '__s1' if (lt(*__s2, *__s1)) ^ /usr/include/c++/v1/__string:135:35: error: unknown type name 'char_type' char_traits<_CharT>::length(const char_type* __s) ^ /usr/include/c++/v1/__string:135:22: error: out-of-line definition of 'length' from class 'char_traits<_CharT>' without definition char_traits<_CharT>::length(const char_type* __s) ~~~~~~~~~~~~~~~~~~~~~^ /usr/include/c++/v1/__string:138:22: error: use of undeclared identifier 'char_type' for (; !eq(*__s, char_type(0)); ++__s) ^ /usr/include/c++/v1/__string:138:17: error: use of undeclared identifier '__s' for (; !eq(*__s, char_type(0)); ++__s) ^ /usr/include/c++/v1/__string:138:39: error: use of undeclared identifier '__s' for (; !eq(*__s, char_type(0)); ++__s) ^ /usr/include/c++/v1/__string:146:33: error: unknown type name 'char_type' char_traits<_CharT>::find(const char_type* __s, size_t __n, const char_type& __a) ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[3]: *** [Makefile:556: treekin-main.o] Error 1 make[3]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1/src' make[2]: *** [Makefile:411: all-recursive] Error 1 make[2]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' gmake[1]: *** [Makefile:344: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/treekin/work/Treekin-0.5.1' ===> 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/treekin build of biology/treekin | treekin-0.5.1_2 ended at Thu Jul 9 18:59:17 CEST 2020 build time: 00:00:14 !!! build failure encountered !!!