Date: Tue, 5 Feb 2019 02:59:32 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-mips-default][biology/dsr-pdb] Failed for dsr-pdb-1.0.3 in build Message-ID: <201902050259.x152xWLF012362@beefy7.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Last committer: yuri@FreeBSD.org Ident: $FreeBSD: head/biology/dsr-pdb/Makefile 491546 2019-01-29 07:56:30Z yuri $ Log URL: http://beefy7.nyi.freebsd.org/data/head-mips-default/p492184_s343758/logs/dsr-pdb-1.0.3.log Build URL: http://beefy7.nyi.freebsd.org/build.html?mastername=head-mips-default&build=p492184_s343758 Log: =>> Building biology/dsr-pdb build started at Tue Feb 5 02:58:09 UTC 2019 port directory: /usr/ports/biology/dsr-pdb package name: dsr-pdb-1.0.3 building for: FreeBSD head-mips-default-job-19 13.0-CURRENT FreeBSD 13.0-CURRENT 1300010 mips maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/dsr-pdb/Makefile 491546 2019-01-29 07:56:30Z yuri $ Poudriere version: 3.2.8 Host OSVERSION: 1300009 Jail OSVERSION: 1300010 Job Id: 19 !!! Jail is newer than host. (Jail: 1300010, Host: 1300009) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=mips UNAME_m=mips ABI_FILE=/usr/lib/crt1.o OSVERSION=1300010 UNAME_v=FreeBSD 13.0-CURRENT 1300010 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/head-mips-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-mips-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-mips-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-mips-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 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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -EB -mabi=32 " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -fPIC " 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--- .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=mips MACHINE_ARCH=mips 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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=Using built-in specs. Target: mips-undermydesk-freebsd Configured with: FreeBSD/mips system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-EB" "-EB" "-melf32btsmip_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_9d218390_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_9d218390_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_9d218390_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_9d218390_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_9d218390_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_9d218390=none ARCH=mips OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300010 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--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as 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) 131072 stack size (kbytes, -s) 8192 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License LGPL21 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> dsr-pdb-1.0.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-mips-default-job-19] Installing pkg-1.10.5_5... [head-mips-default-job-19] Extracting pkg-1.10.5_5: .......... done ===> dsr-pdb-1.0.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of dsr-pdb-1.0.3 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by dsr-pdb-1.0.3 for building =========================================================================== =======================<phase: checksum >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by dsr-pdb-1.0.3 for building => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by dsr-pdb-1.0.3 for building ===> Extracting for dsr-pdb-1.0.3 => SHA256 Checksum OK for dsr-pdb-1.0.3/dsr-pdb.tgz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for dsr-pdb-1.0.3 ===> Applying FreeBSD patches for dsr-pdb-1.0.3 =========================================================================== =======================<phase: build-depends >============================ ===> dsr-pdb-1.0.3 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz [head-mips-default-job-19] Installing gmake-4.2.1_3... [head-mips-default-job-19] `-- Installing gettext-runtime-0.19.8.1_2... [head-mips-default-job-19] | `-- Installing indexinfo-0.3.1... [head-mips-default-job-19] | `-- Extracting indexinfo-0.3.1: .... done [head-mips-default-job-19] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [head-mips-default-job-19] Extracting gmake-4.2.1_3: .......... done ===> dsr-pdb-1.0.3 depends on executable: gmake - found ===> Returning to build of dsr-pdb-1.0.3 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for dsr-pdb-1.0.3 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/aclocal.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/configure configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether /nxb-bin/usr/bin/c++ accepts -g... yes checking for style of include used by gmake... GNU checking dependency style of /nxb-bin/usr/bin/c++... gcc3 checking for gcc... /nxb-bin/usr/bin/cc checking whether we are using the GNU C compiler... yes checking whether /nxb-bin/usr/bin/cc accepts -g... yes 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... mips-portbld-freebsd13.0 checking host system type... mips-portbld-freebsd13.0 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... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /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) 262144 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... no 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 (/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 /nxb-bin/usr/bin/c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the /nxb-bin/usr/bin/c++ linker (/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 (/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... no checking for boost/program_options.hpp... no checking for main in -lboost_program_options... no 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 Boost program_options library not found. Command line arguments to programs will be heavily limited (and lightly tested). ImageMagick++ not found, writing of images will be disabled. =========================================================================== =======================<phase: build >============================ ===> Building for dsr-pdb-1.0.3 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 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -fPIC -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 -O2 -pipe -G0 -EB -mabi=32 -msoft-float -fno-strict-aliasing -fPIC -MT Residue.lo -MD -MP -MF .deps/Residue.Tpo -c Residue.cc -fPIC -DPIC -o .libs/Residue.o In file included from ../include/dsrpdb/Residue.h:24, from Residue.cc:21: ./include/dsrpdb/Point.h: In member function 'double dsrpdb::Point::operator[](unsigned int) const': ./include/dsrpdb/Point.h:69: error: 'assert' was not declared in this scope gmake[3]: *** [Makefile:281: Residue.lo] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/dsr-pdb/work/dsr-pdb-1.0.3/lib' 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
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