From owner-freebsd-pkg-fallout@freebsd.org Wed Nov 27 14:53:03 2019 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id B54671AE320 for ; Wed, 27 Nov 2019 14:53:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 47NNzz59rmz496h for ; Wed, 27 Nov 2019 14:53:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id B15C61AE31E; Wed, 27 Nov 2019 14:53:03 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id B00AE1AE31D for ; Wed, 27 Nov 2019 14:53:03 +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) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 47NNzz4z08z496g for ; Wed, 27 Nov 2019 14:53:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (thunderx1.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fb]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 8D3E5F0CD for ; Wed, 27 Nov 2019 14:53:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (localhost [127.0.0.1]) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id xAREr3KM027990 for ; Wed, 27 Nov 2019 14:53:03 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2/Submit) id xAREr3fN027989; Wed, 27 Nov 2019 14:53:03 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 27 Nov 2019 14:53:03 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201911271453.xAREr3fN027989@thunderx1.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-arm64-default][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_4 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 27 Nov 2019 14:53:03 -0000 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 Last committer: jbeich@FreeBSD.org Ident: $FreeBSD: head/biology/dsr-pdb/Makefile 509290 2019-08-19 15:35:27Z jbeich $ Log URL: http://thunderx1.nyi.freebsd.org/data/head-arm64-default/p518178_s355024/logs/dsr-pdb-1.0.3_4.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p518178_s355024 Log: =>> Building biology/dsr-pdb build started at Wed Nov 27 14:48:33 UTC 2019 port directory: /usr/ports/biology/dsr-pdb package name: dsr-pdb-1.0.3_4 building for: FreeBSD head-arm64-default-job-21 13.0-CURRENT FreeBSD 13.0-CURRENT 1300061 arm64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/dsr-pdb/Makefile 509290 2019-08-19 15:35:27Z jbeich $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300002 Jail OSVERSION: 1300061 Job Id: 21 !!! Jail is newer than host. (Jail: 1300061, Host: 1300002) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300061 UNAME_v=FreeBSD 13.0-CURRENT 1300061 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-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- 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 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=262144 --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 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="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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=13.0 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 9.0.0 (tags/RELEASE_900/final 372316) (based on LLVM 9.0.0) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300061 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License LGPL21 accepted by the user =========================================================================== =================================================== ===> dsr-pdb-1.0.3_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz [head-arm64-default-job-21] Installing pkg-1.12.0... [head-arm64-default-job-21] Extracting pkg-1.12.0: .......... done ===> dsr-pdb-1.0.3_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of dsr-pdb-1.0.3_4 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by dsr-pdb-1.0.3_4 for building =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by dsr-pdb-1.0.3_4 for building => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by dsr-pdb-1.0.3_4 for building ===> Extracting for dsr-pdb-1.0.3_4 => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for dsr-pdb-1.0.3_4 ===> Applying FreeBSD patches for dsr-pdb-1.0.3_4 =========================================================================== =================================================== ===> dsr-pdb-1.0.3_4 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [head-arm64-default-job-21] Installing gmake-4.2.1_3... [head-arm64-default-job-21] `-- Installing gettext-runtime-0.20.1... [head-arm64-default-job-21] | `-- Installing indexinfo-0.3.1... [head-arm64-default-job-21] | `-- Extracting indexinfo-0.3.1: .... done [head-arm64-default-job-21] `-- Extracting gettext-runtime-0.20.1: .......... done [head-arm64-default-job-21] Extracting gmake-4.2.1_3: .......... done ===> dsr-pdb-1.0.3_4 depends on executable: gmake - found ===> Returning to build of dsr-pdb-1.0.3_4 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) 262144 checking command to parse /usr/bin/nm output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc static flag works... yes checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd13.0 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 c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC checking if c++ PIC flag -fPIC works... yes checking if c++ supports -c -o file.o... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.0 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_4 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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 In file included from align.cc:5: In file included from ../include/dsrpdb_internal/align_points.h:6: In file included from ../include/tnt/tnt_array2d.h:31: ./include/tnt/tnt_array1d.h:238:15: warning: '&&' within '||' [-Wlogical-op-parentheses] if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ~~~~~~~~~^~~~~~~~~~~~ ~~ ./include/tnt/tnt_array1d.h:238:15: note: place parentheses around the '&&' expression to silence this warning if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ^ ( ) 1 warning generated. c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 In file included from distance.cc:1: In file included from ../include/dsrpdb/distance.h:28: In file included from ../include/dsrpdb/Matrix.h:4: In file included from ../include/tnt/tnt_array2d.h:31: ./include/tnt/tnt_array1d.h:238:15: warning: '&&' within '||' [-Wlogical-op-parentheses] if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ~~~~~~~~~^~~~~~~~~~~~ ~~ ./include/tnt/tnt_array1d.h:238:15: note: place parentheses around the '&&' expression to silence this warning if ((i0 > 0) && (i1 < n_) || (i0 <= i1)) ^ ( ) 1 warning generated. c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -pg -isystem /usr/local/include -O2 -pipe -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 c++ -O2 -pipe -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 c++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include -isystem /usr/local/include -O2 -pipe -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 c++ -O2 -pipe -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 c++ -O2 -pipe -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 by Protein.cc >>> Protein.o:(dsrpdb::Protein::sequence() const) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::number_of_atoms() const) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::number_of_bonds() const) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::dump(std::__1::basic_ostream >&) const) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::new_residue(dsrpdb::Residue const&)) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::atoms_begin()) in archive ../lib/.libs/libdsrpdb.a >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::atoms_end()) in archive ../lib/.libs/libdsrpdb.a >>> referenced 121 more times 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