From nobody Thu Dec 02 10:13:19 2021 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id B7BB618C4072 for ; Thu, 2 Dec 2021 10:13:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4J4WxW3zR7z4ytj for ; Thu, 2 Dec 2021 10:13:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy7.nyi.freebsd.org (beefy7.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:16]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 6A4C41B4C6 for ; Thu, 2 Dec 2021 10:13:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy7.nyi.freebsd.org (localhost [127.0.0.1]) by beefy7.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 1B2ADJSB095991 for ; Thu, 2 Dec 2021 10:13:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy7.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 1B2ADJ4o095990; Thu, 2 Dec 2021 10:13:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 2 Dec 2021 10:13:19 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202112021013.1B2ADJ4o095990@beefy7.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - main-riscv64-default][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_5 in build ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1638439999; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=DSP9p94WHrSBAKEo7PD8mi00ejXZIts2BBS0eSpApEM=; b=RbDoLwNiOFOIqUX1cMw7TgphlZzQ1K+Xu5bqrTF0zBDOfpVPBjuiP7oCcmLurAxpbAGQ8T qmGRHWyuyf7IJu1c6gwCHnuAHg3hc9UUNyLKQnoprXtC4/mTvrtpZWSdbn1lOmijRQfdJs ge0V2H0sRXGTACdN++bZgZiaLTNrBg9Doe0vBzeg7reWQ6TVqs0tnUTY+S+5dqeLnl8Yzw WA+CQ4blKjOmFm9kFXcYgE4Jfa9Pi2DHbvqA0py9SxAETzDqo/Swn2I3VVpXTE8hTBC/P7 df1a0973hgSxzT/BoZasCr5NAsF2IvOEC241OeABKhN+azH1CByZ9RoUsCAfRA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1638439999; a=rsa-sha256; cv=none; b=u2G68RmeVPL07BLsJUHT3Cu/OtnGaPaefWgtI2AdOI9V1KnDOiebEhY7ZVErAprV1UouHi iS6vlwoKd53aXQM3yOgXg7EcjpECAu6YQjEsBPo2mmGXVdg0yPl6GRilBqPF57gaCc+j3I uH7QFOTC/b7CixsNKmuAm/SSr5UGDowEY99L4ajLAUXI8ea/rOwy2X4FCmMAnollvz4OfT DPcYXPeA4CGQfyUznegauJ7n8hAIgkzoGsYtOQug9fm2LBnJfrVR2aNQsG7V/NEdNtPRdH IEB/UlGarogjbaJxGO3JAHFzQHwNCGnb87OQcbN5gDD7xtTtmOgsaJaQgaihyA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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: yuri@FreeBSD.org Log URL: http://beefy7.nyi.freebsd.org/data/main-riscv64-default/p401d71441a09_sf16ec9c6e3/logs/dsr-pdb-1.0.3_5.log Build URL: http://beefy7.nyi.freebsd.org/build.html?mastername=main-riscv64-default&build=p401d71441a09_sf16ec9c6e3 Log: =>> Building biology/dsr-pdb build started at Thu Dec 2 10:11:21 UTC 2021 port directory: /usr/ports/biology/dsr-pdb package name: dsr-pdb-1.0.3_5 building for: FreeBSD main-riscv64-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400043 riscv maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400008 Jail OSVERSION: 1400043 Job Id: 08 !!! Jail is newer than host. (Jail: 1400043, Host: 1400008) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=riscv64 UNAME_m=riscv ABI_FILE=/usr/lib/crt1.o OSVERSION=1400043 UNAME_v=FreeBSD 14.0-CURRENT 1400043 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/main-riscv64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-riscv64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-riscv64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-riscv64-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-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work/.cache HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/dsr-pdb/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work/.cache HOME=/wrkdirs/usr/ports/biology/dsr-pdb/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/dsr-pdb/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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -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=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/dsr-pdb" EXAMPLESDIR="share/examples/dsr-pdb" DATADIR="share/dsr-pdb" WWWDIR="www/dsr-pdb" ETCDIR="etc/dsr-pdb" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/dsr-pdb DOCSDIR=/usr/local/share/doc/dsr-pdb EXAMPLESDIR=/usr/local/share/examples/dsr-pdb WWWDIR=/usr/local/www/dsr-pdb ETCDIR=/usr/local/etc/dsr-pdb --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=riscv MACHINE_ARCH=riscv64 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_9d218390=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: riscv64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: riscv64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-m" "elf64lriscv" "-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: riscv64-unknown-freebsd14.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=riscv64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400043 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 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 LGPL21 accepted by the user =========================================================================== =================================================== ===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg pkg-static: Warning: Major OS version upgrade detected. Running "pkg bootstrap -f" recommended [main-riscv64-default-job-08] Installing pkg-1.17.5... [main-riscv64-default-job-08] Extracting pkg-1.17.5: .......... done ===> dsr-pdb-1.0.3_5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of dsr-pdb-1.0.3_5 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by dsr-pdb-1.0.3_5 for building =========================================================================== =================================================== ===> License LGPL21 accepted by the user checking for /nxb-bin/usr/bin/cc option to accept ANSI C... none needed checking dependency style of /nxb-bin/usr/bin/cc... gcc3 checking how to run the C preprocessor... /nxb-bin/usr/bin/cpp checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether gmake sets $(MAKE)... (cached) yes checking build system type... riscv64-portbld-freebsd14.0 checking host system type... riscv64-portbld-freebsd14.0 checking for a sed that does not truncate output... /usr/bin/sed checking for egrep... grep -E checking for ld used by /nxb-bin/usr/bin/cc... /nxb-bin/usr/bin/ld checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes checking for /nxb-bin/usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm checking how to recognise dependent libraries... pass_all 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 dlfcn.h... (cached) yes checking how to run the C++ preprocessor... /nxb-bin/usr/bin/c++ -E checking for g77... no checking for f77... no checking for xlf... no checking for frt... no checking for pgf77... no checking for fort77... no checking for fl32... no checking for af77... no checking for f90... no checking for xlf90... no checking for pgf90... no checking for epcf90... no checking for f95... no checking for fort... no checking for xlf95... no checking for ifc... no checking for efc... no checking for pgf95... no checking for lf95... no checking for gfortran... no checking whether we are using the GNU Fortran 77 compiler... no checking whether accepts -g... no checking the maximum length of command line arguments... (cached) 524288 checking command to parse /usr/bin/nm output from /nxb-bin/usr/bin/cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if /nxb-bin/usr/bin/cc static flag works... yes checking if /nxb-bin/usr/bin/cc supports -fno-rtti -fno-exceptions... yes checking for /nxb-bin/usr/bin/cc option to produce PIC... -fPIC checking if /nxb-bin/usr/bin/cc PIC flag -fPIC works... yes checking if /nxb-bin/usr/bin/cc supports -c -o file.o... yes checking whether the /nxb-bin/usr/bin/cc linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd14.0 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by /nxb-bin/usr/bin/c++... /nxb-bin/usr/bin/ld checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes checking for /nxb-bin/usr/bin/c++ option to produce PIC... -fPIC checking if /nxb-bin/usr/bin/c++ PIC flag -fPIC works... yes checking if /nxb-bin/usr/bin/c++ supports -c -o file.o... yes checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.0 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes appending configuration tag "F77" to libtool checking CGAL_MAKEFILE... no checking CGAL/Exact_predicates_inexact_constructions_kernel.h usability... no checking CGAL/Exact_predicates_inexact_constructions_kernel.h presence... no checking for CGAL/Exact_predicates_inexact_constructions_kernel.h... no checking CGAL... no checking boost/program_options.hpp usability... no checking boost/program_options.hpp presence... yes configure: WARNING: boost/program_options.hpp: present but cannot be compiled configure: WARNING: boost/program_options.hpp: check for missing prerequisite headers? configure: WARNING: boost/program_options.hpp: see the Autoconf documentation configure: WARNING: boost/program_options.hpp: section "Present But Cannot Be Compiled" configure: WARNING: boost/program_options.hpp: proceeding with the preprocessor's result configure: WARNING: boost/program_options.hpp: in the future, the compiler will take precedence configure: WARNING: ## -------------------------------------------- ## configure: WARNING: ## Report this to drussel@graphics.stanford.edu ## configure: WARNING: ## -------------------------------------------- ## checking for boost/program_options.hpp... yes checking for main in -lboost_program_options... yes checking for main in -lMagick++... no checking Magick++.h usability... no checking Magick++.h presence... no checking for Magick++.h... no configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating include/Makefile config.status: creating include/dsrpdb/Makefile config.status: creating include/dsrpdb_internal/Makefile config.status: creating include/tnt/Makefile config.status: creating lib/Makefile config.status: creating test/Makefile config.status: creating tools/Makefile config.status: creating config.h config.status: executing depfiles commands ImageMagick++ not found, writing of images will be disabled. =========================================================================== =================================================== ===> Building for dsr-pdb-1.0.3_5 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' gmake all-recursive gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' Making all in lib gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF ".deps/Residue.Tpo" -c -o Residue.lo Residue.cc; \ then mv -f ".deps/Residue.Tpo" ".deps/Residue.Plo"; else rm -f ".deps/Residue.Tpo"; exit 1; fi mkdir .libs /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF .deps/Residue.Tpo -c Residue.cc -fPIC -DPIC -o .libs/Residue.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue.lo -MD -MP -MF .deps/Residue.Tpo -c Residue.cc -o Residue.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF ".deps/Protein.Tpo" -c -o Protein.lo Protein.cc; \ then mv -f ".deps/Protein.Tpo" ".deps/Protein.Plo"; else rm -f ".deps/Protein.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF .deps/Protein.Tpo -c Protein.cc -fPIC -DPIC -o .libs/Protein.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein.lo -MD -MP -MF .deps/Protein.Tpo -c Protein.cc -o Protein.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF ".deps/Residue_data.Tpo" -c -o Residue_data.lo Residue_data.cc; \ then mv -f ".deps/Residue_data.Tpo" ".deps/Residue_data.Plo"; else rm -f ".deps/Residue_data.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF .deps/Residue_data.Tpo -c Residue_data.cc -fPIC -DPIC -o .libs/Residue_data.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Residue_data.lo -MD -MP -MF .deps/Residue_data.Tpo -c Residue_data.cc -o Residue_data.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF ".deps/Protein_pdb.Tpo" -c -o Protein_pdb.lo Protein_pdb.cc; \ then mv -f ".deps/Protein_pdb.Tpo" ".deps/Protein_pdb.Plo"; else rm -f ".deps/Protein_pdb.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF .deps/Protein_pdb.Tpo -c Protein_pdb.cc -fPIC -DPIC -o .libs/Protein_pdb.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Protein_pdb.lo -MD -MP -MF .deps/Protein_pdb.Tpo -c Protein_pdb.cc -o Protein_pdb.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF ".deps/pdb_utils.Tpo" -c -o pdb_utils.lo pdb_utils.cc; \ then mv -f ".deps/pdb_utils.Tpo" ".deps/pdb_utils.Plo"; else rm -f ".deps/pdb_utils.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF .deps/pdb_utils.Tpo -c pdb_utils.cc -fPIC -DPIC -o .libs/pdb_utils.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_utils.lo -MD -MP -MF .deps/pdb_utils.Tpo -c pdb_utils.cc -o pdb_utils.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF ".deps/Model.Tpo" -c -o Model.lo Model.cc; \ then mv -f ".deps/Model.Tpo" ".deps/Model.Plo"; else rm -f ".deps/Model.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF .deps/Model.Tpo -c Model.cc -fPIC -DPIC -o .libs/Model.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Model.lo -MD -MP -MF .deps/Model.Tpo -c Model.cc -o Model.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF ".deps/PDB.Tpo" -c -o PDB.lo PDB.cc; \ then mv -f ".deps/PDB.Tpo" ".deps/PDB.Plo"; else rm -f ".deps/PDB.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF .deps/PDB.Tpo -c PDB.cc -fPIC -DPIC -o .libs/PDB.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT PDB.lo -MD -MP -MF .deps/PDB.Tpo -c PDB.cc -o PDB.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF ".deps/align.Tpo" -c -o align.lo align.cc; \ then mv -f ".deps/align.Tpo" ".deps/align.Plo"; else rm -f ".deps/align.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF .deps/align.Tpo -c align.cc -fPIC -DPIC -o .libs/align.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT align.lo -MD -MP -MF .deps/align.Tpo -c align.cc -o align.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF ".deps/distance.Tpo" -c -o distance.lo distance.cc; \ then mv -f ".deps/distance.Tpo" ".deps/distance.Plo"; else rm -f ".deps/distance.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF .deps/distance.Tpo -c distance.cc -fPIC -DPIC -o .libs/distance.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT distance.lo -MD -MP -MF .deps/distance.Tpo -c distance.cc -o distance.o >/dev/null 2>&1 if /bin/sh ../libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF ".deps/Error_logger.Tpo" -c -o Error_logger.lo Error_logger.cc; \ then mv -f ".deps/Error_logger.Tpo" ".deps/Error_logger.Plo"; else rm -f ".deps/Error_logger.Tpo"; exit 1; fi /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF .deps/Error_logger.Tpo -c Error_logger.cc -fPIC -DPIC -o .libs/Error_logger.o /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT Error_logger.lo -MD -MP -MF .deps/Error_logger.Tpo -c Error_logger.cc -o Error_logger.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link /nxb-bin/usr/bin/c++ -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o libdsrpdb.la -rpath /usr/local/lib -static Residue.lo Protein.lo Residue_data.lo Protein_pdb.lo pdb_utils.lo Model.lo PDB.lo align.lo distance.lo Error_logger.lo ar cru .libs/libdsrpdb.a Residue.o Protein.o Residue_data.o Protein_pdb.o pdb_utils.o Model.o PDB.o align.o distance.o Error_logger.o ranlib .libs/libdsrpdb.a creating libdsrpdb.la (cd .libs && rm -f libdsrpdb.la && ln -s ../libdsrpdb.la libdsrpdb.la) gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' Making all in tools gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' if /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -MT pdb_stats.o -MD -MP -MF ".deps/pdb_stats.Tpo" -c -o pdb_stats.o pdb_stats.cc; \ then mv -f ".deps/pdb_stats.Tpo" ".deps/pdb_stats.Po"; else rm -f ".deps/pdb_stats.Tpo"; exit 1; fi /bin/sh ../libtool --tag=CXX --mode=link /nxb-bin/usr/bin/c++ -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -lboost_program_options -o pdb_stats pdb_stats.o ../lib/libdsrpdb.la mkdir .libs /nxb-bin/usr/bin/c++ -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC --std=c++11 -isystem /usr/local/include -fstack-protector-strong -o pdb_stats pdb_stats.o -L/usr/local/lib ../lib/.libs/libdsrpdb.a -lboost_program_options ld: error: undefined symbol: _mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::Protein()) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::chain() const) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::set_chain(char)) in archive ../lib/.libs/libdsrpdb.a >>> referenced 141 more times >>> did you mean: _mount >>> defined in: /lib/libc.so.7 c++: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: *** [Makefile:317: pdb_stats] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/tools' gmake[2]: *** [Makefile:250: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' gmake[1]: *** [Makefile:179: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3' *** Error code 1 Stop. make: stopped in /usr/ports/biology/dsr-pdb