From owner-freebsd-pkg-fallout@freebsd.org Thu Dec 24 19:47:18 2020 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 942894CEF9C for ; Thu, 24 Dec 2020 19:47:18 +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 4D20w63l2xz3DX9 for ; Thu, 24 Dec 2020 19:47:18 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 805964CECE2; Thu, 24 Dec 2020 19:47:18 +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 802094CEE3D for ; Thu, 24 Dec 2020 19:47:18 +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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4D20w63DnZz3DPL for ; Thu, 24 Dec 2020 19:47:18 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere1.nyi.freebsd.org (ampere1.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:f5]) (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 61DFC15F79 for ; Thu, 24 Dec 2020 19:47:18 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere1.nyi.freebsd.org (localhost [127.0.0.1]) by ampere1.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 0BOJlIFE016234 for ; Thu, 24 Dec 2020 19:47:18 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere1.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 0BOJlIFU016233; Thu, 24 Dec 2020 19:47:18 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 24 Dec 2020 19:47:18 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202012241947.0BOJlIFU016233@ampere1.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 121arm64-quarterly][biology/dsr-pdb] Failed for dsr-pdb-1.0.3_5 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 24 Dec 2020 19:47:18 -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: branches/2020Q4/biology/dsr-pdb/Makefile 519824 2019-12-11 17:53:48Z jbeich $ Log URL: http://ampere1.nyi.freebsd.org/data/121arm64-quarterly/559008/logs/dsr-pdb-1.0.3_5.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=121arm64-quarterly&build=559008 Log: =>> Building biology/dsr-pdb build started at Thu Dec 24 19:46:07 UTC 2020 port directory: /usr/ports/biology/dsr-pdb package name: dsr-pdb-1.0.3_5 building for: FreeBSD 121arm64-quarterly-job-06 12.1-RELEASE FreeBSD 12.1-RELEASE arm64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: branches/2020Q4/biology/dsr-pdb/Makefile 519824 2019-12-11 17:53:48Z jbeich $ Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1300121 Jail OSVERSION: 1201000 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1201000 UNAME_v=FreeBSD 12.1-RELEASE UNAME_r=12.1-RELEASE 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=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/121arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=121arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/121arm64-quarterly/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=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 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=12.1 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 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 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 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.1-RELEASE OSREL=12.1 OSVERSION=1201000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> 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-1.15.10.txz [121arm64-quarterly-job-06] Installing pkg-1.15.10... [121arm64-quarterly-job-06] Extracting pkg-1.15.10: .......... 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 ===> Fetching all distfiles required by dsr-pdb-1.0.3_5 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_5 for building ===> Extracting for dsr-pdb-1.0.3_5 => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for dsr-pdb-1.0.3_5 ===> Applying FreeBSD patches for dsr-pdb-1.0.3_5 from /usr/ports/biology/dsr-pdb/files =========================================================================== =================================================== ===> dsr-pdb-1.0.3_5 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.txz [121arm64-quarterly-job-06] Installing gmake-4.3_2... [121arm64-quarterly-job-06] `-- Installing gettext-runtime-0.21... [121arm64-quarterly-job-06] | `-- Installing indexinfo-0.3.1... [121arm64-quarterly-job-06] | `-- Extracting indexinfo-0.3.1: .... done [121arm64-quarterly-job-06] `-- Extracting gettext-runtime-0.21: .......... done [121arm64-quarterly-job-06] Extracting gmake-4.3_2: .......... done ===> dsr-pdb-1.0.3_5 depends on package: gmake>=4.3 - found ===> Returning to build of dsr-pdb-1.0.3_5 =========================================================================== =================================================== ===> dsr-pdb-1.0.3_5 depends on shared library: libboost_program_options.so - not found ===> Installing existing package /packages/All/boost-libs-1.72.0_2.txz [121arm64-quarterly-job-06] Installing boost-libs-1.72.0_2... [121arm64-quarterly-job-06] `-- Installing icu-67.1,1... [121arm64-quarterly-job-06] `-- Extracting icu-67.1,1: .......... done [121arm64-quarterly-job-06] Extracting boost-libs-1.72.0_2: .......... done ===== Message from boost-libs-1.72.0_2: ./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)) ^ ( ) 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 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 /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 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_split.o -MD -MP -MF ".deps/pdb_split.Tpo" -c -o pdb_split.o pdb_split.cc; \ then mv -f ".deps/pdb_split.Tpo" ".deps/pdb_split.Po"; else rm -f ".deps/pdb_split.Tpo"; exit 1; fi 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_transform.o -MD -MP -MF ".deps/pdb_transform.Tpo" -c -o pdb_transform.o pdb_transform.cc; \ then mv -f ".deps/pdb_transform.Tpo" ".deps/pdb_transform.Po"; else rm -f ".deps/pdb_transform.Tpo"; exit 1; fi 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_cat.o -MD -MP -MF ".deps/pdb_cat.Tpo" -c -o pdb_cat.o pdb_cat.cc; \ then mv -f ".deps/pdb_cat.Tpo" ".deps/pdb_cat.Po"; else rm -f ".deps/pdb_cat.Tpo"; exit 1; fi 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_align.o -MD -MP -MF ".deps/pdb_align.Tpo" -c -o pdb_align.o pdb_align.cc; \ then mv -f ".deps/pdb_align.Tpo" ".deps/pdb_align.Po"; else rm -f ".deps/pdb_align.Tpo"; exit 1; fi 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_align_points.o -MD -MP -MF ".deps/pdb_align_points.Tpo" -c -o pdb_align_points.o pdb_align_points.cc; \ then mv -f ".deps/pdb_align_points.Tpo" ".deps/pdb_align_points.Po"; else rm -f ".deps/pdb_align_points.Tpo"; exit 1; fi In file included from pdb_align.cc:27: 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)) ^ ( ) In file included from pdb_align_points.cc:28: 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. 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_distance_matrix.o -MD -MP -MF ".deps/pdb_distance_matrix.Tpo" -c -o pdb_distance_matrix.o pdb_distance_matrix.cc; \ then mv -f ".deps/pdb_distance_matrix.Tpo" ".deps/pdb_distance_matrix.Po"; else rm -f ".deps/pdb_distance_matrix.Tpo"; exit 1; fi 1 warning generated. 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_distance.o -MD -MP -MF ".deps/pdb_distance.Tpo" -c -o pdb_distance.o pdb_distance.cc; \ then mv -f ".deps/pdb_distance.Tpo" ".deps/pdb_distance.Po"; else rm -f ".deps/pdb_distance.Tpo"; exit 1; fi In file included from pdb_distance_matrix.cc:25: 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)) ^ ( ) In file included from pdb_distance.cc:27: 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. /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 ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::chain() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::set_chain(char)) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::sequence() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::number_of_atoms() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::number_of_bonds() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::dump(std::__1::basic_ostream >&) const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::new_residue(dsrpdb::Residue const&)) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::atoms_begin()) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::atoms_end()) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::atoms_begin() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::atoms_end() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::bonds_begin() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::bonds_end() const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::residue(dsrpdb::PDB_index) const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::residue_offset(dsrpdb::PDB_index) const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::has_residue(dsrpdb::PDB_index) const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::residue_offset_of_atom_index(dsrpdb::PDB_index) const) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::set_atom(dsrpdb::PDB_index, dsrpdb::Atom const&)) in archive ../lib/.libs/libdsrpdb.a ld: error: undefined symbol: .mcount >>> referenced by Protein.cc >>> Protein.o:(dsrpdb::Protein::atom(dsrpdb::PDB_index) const) in archive ../lib/.libs/libdsrpdb.a ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors) c++: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: *** [Makefile:317: pdb_stats] Error 1 gmake[3]: *** Waiting for unfinished jobs.... 1 warning generated. 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' ===> 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/dsr-pdb