Date: Sat, 4 Mar 2017 02:08:52 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110mips-quarterly][biology/libsbml] Failed for libsbml-5.13.0 in configure Message-ID: <201703040208.v2428qS4030527@beefy14.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: ports@FreeBSD.org Last committer: mat@FreeBSD.org Ident: $FreeBSD: branches/2017Q1/biology/libsbml/Makefile 425174 2016-11-02 22:45:14Z mat $ Log URL: http://beefy14.nyi.freebsd.org/data/110mips-quarterly/435355/logs/libsbml-5.13.0.log Build URL: http://beefy14.nyi.freebsd.org/build.html?mastername=110mips-quarterly&build=435355 Log: ====>> Building biology/libsbml build started at Sat Mar 4 02:07:36 UTC 2017 port directory: /usr/ports/biology/libsbml building for: FreeBSD 110mips-quarterly-job-22 11.0-RELEASE-p8 FreeBSD 11.0-RELEASE-p8 r314125 mips maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: branches/2017Q1/biology/libsbml/Makefile 425174 2016-11-02 22:45:14Z mat $ Poudriere version: 3.1.14 Host OSVERSION: 1200020 Jail OSVERSION: 1100122 Job Id: 22 ---Begin Environment--- SHELL=/bin/csh UNAME_p=mips UNAME_m=mips ABI_FILE=/usr/lib/crt1.o OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p8 r314125 UNAME_r=11.0-RELEASE-p8 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110mips-quarterly/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=libsbml-5.13.0 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110mips-quarterly/ref/.p/pool MASTERNAME=110mips-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for libsbml-5.13.0: EXAMPLES=on: Build and/or install examples PYTHON=off: Python bindings or support RUBY=off: Ruby bindings or support ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsbml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsbml/work HOME=/wrkdirs/usr/ports/biology/libsbml/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/libsbml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/libsbml/work HOME=/wrkdirs/usr/ports/biology/libsbml/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" -L/usr/lib" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTVERSION=5.13.0 EXAMPLES="" NO_EXAMPLES="@comment " PYTHON="@comment " NO_PYTHON="" RUBY="@comment " NO_RUBY="" CMAKE_BUILD_TYPE="release" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/libsbml" EXAMPLESDIR="share/examples/libsbml" DATADIR="share/libsbml" WWWDIR="www/libsbml" ETCDIR="etc/libsbml" --End PLIST_SUB-- --SUB_LIST-- EXAMPLES="" NO_EXAMPLES="@comment " PYTHON="@comment " NO_PYTHON="" RUBY="@comment " NO_RUBY="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/libsbml DOCSDIR=/usr/local/share/doc/libsbml EXAMPLESDIR=/usr/local/share/examples/libsbml WWWDIR=/usr/local/www/libsbml ETCDIR=/usr/local/etc/libsbml --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 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 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=mips CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native\|linux _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ _OSRELEASE=11.0-RELEASE-p8 #### Misc Poudriere #### GID=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 READELF=/nxb-bin/usr/bin/readelf 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 >============================ ===> NOTICE: The libsbml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License LGPL21 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> libsbml-5.13.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz [110mips-quarterly-job-22] Installing pkg-1.9.4_1... [110mips-quarterly-job-22] Extracting pkg-1.9.4_1: .......... done <snip> =========================================================================== =======================<phase: extract >============================ ===> NOTICE: The libsbml port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by libsbml-5.13.0 for building ===> Extracting for libsbml-5.13.0 => SHA256 Checksum OK for libSBML-5.13.0-core-src.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for libsbml-5.13.0 =========================================================================== =======================<phase: build-depends >============================ ===> libsbml-5.13.0 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.7.1.txz [110mips-quarterly-job-22] Installing cmake-3.7.1... [110mips-quarterly-job-22] `-- Installing expat-2.2.0_1... [110mips-quarterly-job-22] `-- Extracting expat-2.2.0_1: .......... done [110mips-quarterly-job-22] `-- Installing cmake-modules-3.7.1... [110mips-quarterly-job-22] `-- Extracting cmake-modules-3.7.1: .......... done [110mips-quarterly-job-22] `-- Installing curl-7.53.0... [110mips-quarterly-job-22] | `-- Installing libnghttp2-1.18.0... [110mips-quarterly-job-22] | `-- Extracting libnghttp2-1.18.0: .......... done [110mips-quarterly-job-22] | `-- Installing ca_root_nss-3.29.1... [110mips-quarterly-job-22] | `-- Extracting ca_root_nss-3.29.1: ........ done [110mips-quarterly-job-22] `-- Extracting curl-7.53.0: .......... done [110mips-quarterly-job-22] `-- Installing libarchive-3.2.2,1... [110mips-quarterly-job-22] | `-- Installing liblz4-131... [110mips-quarterly-job-22] | `-- Extracting liblz4-131: .......... done [110mips-quarterly-job-22] | `-- Installing lzo2-2.09... [110mips-quarterly-job-22] | `-- Extracting lzo2-2.09: .......... done [110mips-quarterly-job-22] `-- Extracting libarchive-3.2.2,1: .......... done [110mips-quarterly-job-22] `-- Installing jsoncpp-1.8.0_1... [110mips-quarterly-job-22] `-- Extracting jsoncpp-1.8.0_1: .......... done [110mips-quarterly-job-22] `-- Installing libuv-1.10.1... [110mips-quarterly-job-22] `-- Extracting libuv-1.10.1: .......... done [110mips-quarterly-job-22] Extracting cmake-3.7.1: .......... done Message from ca_root_nss-3.29.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> libsbml-5.13.0 depends on file: /usr/local/bin/cmake - found ===> Returning to build of libsbml-5.13.0 =========================================================================== =======================<phase: lib-depends >============================ ===> libsbml-5.13.0 depends on shared library: libxml2.so - not found ===> Installing existing package /packages/All/libxml2-2.9.4.txz [110mips-quarterly-job-22] Installing libxml2-2.9.4... [110mips-quarterly-job-22] Extracting libxml2-2.9.4: .......... done ===> libsbml-5.13.0 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> Returning to build of libsbml-5.13.0 =========================================================================== =======================<phase: configure >============================ ===> Configuring for libsbml-5.13.0 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.13.0/config/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.13.0/configure ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/libsbml/work/.build -- The C compiler identification is GNU 4.2.1 -- The CXX compiler identification is GNU 4.2.1 -- Check for working C compiler: /nxb-bin/usr/bin/cc -- Check for working C compiler: /nxb-bin/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /nxb-bin/usr/bin/cc -- works -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR) -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Looking for gzopen in /usr/lib/libz.so -- Looking for gzopen in /usr/lib/libz.so - found -- Looking for include file check.h -- Looking for include file check.h - not found -- Looking for include file expat.h -- Looking for include file expat.h - not found -- Looking for include file errno.h -- Looking for include file errno.h - found -- Looking for include file ieeefp.h CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_c8d92/fast" -- Looking for include file ieeefp.h - not found -- Looking for include file math.h CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_0da20/fast" -- Looking for include file math.h - not found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file float.h -- Looking for include file float.h - found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - big endian -- Looking for sqrt in m CMake Error: Generator: execution of make failed. Make command was: "/usr/bin/make" "cmTC_223f9/fast" -- Looking for sqrt in m - not found -- ---------------------------------------------------------------------- libSBML version 5.13.0 ---------------------------------------------------------------------- More information and the latest version are available online at http://sbml.org/Software/libSBML Please report problems using the issue tracker at http://sbml.org/Software/libsbml/issue-tracker To contact the developers directly, email libsbml-team@caltech.edu Configured on host '110mips-quarterly-job-22' host type = FreeBSD host operating system = FreeBSD 11.0-RELEASE-p8 host CPU architecture = mips General build flags: CC = /nxb-bin/usr/bin/cc CXX = /nxb-bin/usr/bin/c++ CPPFLAGS = -DLINUX CFLAGS = -O2 -pipe -G0 -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -fno-strict-aliasing -fPIC CXXFLAGS = -O2 -pipe -G0 -I/usr/include -DLIBICONV_PLUG -fno-strict-aliasing -DLIBICONV_PLUG -fno-strict-aliasing -fPIC LDFLAGS = -L/usr/lib XML parser library configuration: XML library = libxml2 CPPFLAGS for XML = -I/usr/local/include/libxml2 LIBS for XML = /usr/local/lib/libxml2.so Other libSBML configuration settings: Installation $prefix = /usr/local -- Value of $LD_LIBRARY_PATH = -- Using SWIG = SWIG_EXECUTABLE-NOTFOUND (Version ) -- Using C++ namespace ('libsbml') = no -- -- Build examples = no -- -- Use Legacy Math = no -- -- Support for SBML Level 3 Packages: -- SBML 'layout' package = OFF -- -- Other potentially important settings: -- Compression support is enabled for .zip and .gz files -- Compression support is enabled for .bz2 files -- ---------------------------------------------------------------------- -- Configuring incomplete, errors occurred! See also "/wrkdirs/usr/ports/biology/libsbml/work/.build/CMakeFiles/CMakeOutput.log". See also "/wrkdirs/usr/ports/biology/libsbml/work/.build/CMakeFiles/CMakeError.log". *** Error code 1 Stop. make: stopped in /usr/ports/biology/libsbml
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