[REL - head-i386-default][biology/lamarc] Failed for lamarc-2.1.8, 1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Oct 3 12:35:33 UTC 2013
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 at FreeBSD.org
Last committer: bdrewery at FreeBSD.org
Ident: $FreeBSD: head/biology/lamarc/Makefile 328226 2013-09-25 00:54:08Z bdrewery $
Log URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-10-03_03h09m26s/logs/lamarc-2.1.8,1.log
Build URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-10-03_03h09m26s
Log:
====>> Building biology/lamarc
build started at Thu Oct 3 12:35:11 UTC 2013
port directory: /usr/ports/biology/lamarc
building for: FreeBSD head-i386-default-job-23 10.0-CURRENT FreeBSD 10.0-CURRENT i386
maintained by: ports at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/lamarc/Makefile 328226 2013-09-25 00:54:08Z bdrewery $
Poudriere version: 3.1-pre
---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=1000055
UNAME_v=FreeBSD 10.0-CURRENT
UNAME_r=10.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
STATUS=1
MASTERMNT=/usr/local/poudriere/data/build/head-i386-default/ref
PKG_EXT=txz
tpid=26968
POUDRIERE_BUILD_TYPE=bulk
NBPARALLEL=24
PKGNG=1
PKGNAME=lamarc-2.1.8,1
PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f
PKG_ADD=/usr/local/sbin/pkg-static add
PWD=/root
MASTERNAME=head-i386-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
PKG_VERSION=/poudriere/pkg-static version
---End Environment---
---Begin OPTIONS List---
===> The following configuration options are available for lamarc-2.1.8,1:
DOCS=on: Build and/or install documentation
WXGTK=off: wxGTK GUI toolkit support
===> Use 'make config' to modify these settings
---End OPTIONS List---
--CONFIGURE_ARGS--
--disable-converter --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
TMPDIR="/tmp" TMPDIR="/tmp" 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--
TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444"
--End MAKE_ENV--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/lamarc
DOCSDIR=/usr/local/share/doc/lamarc
EXAMPLESDIR=/usr/local/share/examples/lamarc
WWWDIR=/usr/local/www/lamarc
ETCDIR=/usr/local/etc/lamarc
--End SUB_LIST--
---Begin make.conf---
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=yes
---End make.conf---
===> Cleaning for lamarc-2.1.8,1
=======================<phase: check-config >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> lamarc-2.1.8,1 depends on file: /usr/local/sbin/pkg - not found
===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg
===> Installing existing package /packages/All/pkg-1.1.4_6.txz
Installing pkg-1.1.4_6... done
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of lamarc-2.1.8,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License AL2 accepted by the user
===> Fetching all distfiles required by lamarc-2.1.8,1 for building
===========================================================================
=======================<phase: checksum >============================
===> License AL2 accepted by the user
===> Fetching all distfiles required by lamarc-2.1.8,1 for building
=> SHA256 Checksum OK for lamarc-2.1.8-src.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License AL2 accepted by the user
===> Fetching all distfiles required by lamarc-2.1.8,1 for building
===> Extracting for lamarc-2.1.8,1
=> SHA256 Checksum OK for lamarc-2.1.8-src.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for lamarc-2.1.8,1
===> Applying FreeBSD patches for lamarc-2.1.8,1
===========================================================================
=======================<phase: build-depends >============================
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for lamarc-2.1.8,1
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8/aclocal.m4
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8/configure
configure: loading site script /usr/ports/Templates/config.site
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... i386-portbld-freebsd10.0
checking host system type... i386-portbld-freebsd10.0
checking target system type... i386-portbld-freebsd10.0
checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether make 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 c++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of c++... gcc3
checking for ranlib... ranlib
checking for gcc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
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 float.h... (cached) yes
checking for limits.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... (cached) yes
checking for _Bool... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... (cached) yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for error_at_line... no
checking for working memcmp... yes
checking for strftime... (cached) yes
checking for getcwd... (cached) yes
checking for pow... no
checking for sqrt... no
checking for strchr... yes
checking for strpbrk... (cached) yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config/conf.h
config.status: executing depfiles commands
*************************************************************
Settings for lamarc build. For information on how to change
try executing "configure --help" and reading the lamarc
documentation section entitled "Compiling Lamarc".
*************************************************************
Options that are almost always on:
Compile lam_conv, the lamarc data converter? no
Compile lam_conv as a GUI? --
Compile LAMARC to read data? yes
Compile LAMARC to display progress bar? yes
Options that are almost always off:
<snip>
In file included from ./boost/random/uniform_int.hpp:26:
./boost/random/uniform_smallint.hpp:39:63: warning: unused parameter 'ud' [-Wunused-parameter]
InputStream& extract_uniform_int(InputStream& is, UniformInt& ud, Impl& impl)
^
In file included from src/bayeslike/bayesanalyzer_1d.cpp:26:
In file included from ./src/force/force.h:16:
In file included from ./src/postlike/plforces.h:29:
./src/tree/summary.h:33:1: warning: class 'Interval' was previously declared as a struct [-Wmismatched-tags]
class Interval;
^
./src/tree/intervaldata.h:55:8: note: previous use is here
struct Interval
^
./src/tree/summary.h:33:1: note: did you mean struct here?
class Interval;
^~~~~
struct
./src/tree/summary.h:195:52: warning: unused parameter 'totals' [-Wunused-parameter]
virtual void AdjustSummary(const DoubleVec1d & totals, long region) {};
^
./src/tree/summary.h:195:65: warning: unused parameter 'region' [-Wunused-parameter]
virtual void AdjustSummary(const DoubleVec1d & totals, long region) {};
^
In file included from src/bayeslike/bayesanalyzer_1d.cpp:26:
In file included from ./src/force/force.h:16:
./src/postlike/plforces.h:401:45: warning: unused parameter 'param' [-Wunused-parameter]
double DlnWait (const vector < double >¶m,
^
./src/postlike/plforces.h:402:41: warning: unused parameter 'treedata' [-Wunused-parameter]
const TreeSummary * treedata,
^
./src/postlike/plforces.h:403:33: warning: unused parameter 'whichparam' [-Wunused-parameter]
const long &whichparam) { assert(false); return 0;};
^
./src/postlike/plforces.h:405:46: warning: unused parameter 'param' [-Wunused-parameter]
double DlnPoint (const vector < double >¶m,
^
./src/postlike/plforces.h:406:42: warning: unused parameter 'treedata' [-Wunused-parameter]
const TreeSummary * treedata,
^
./src/postlike/plforces.h:407:34: warning: unused parameter 'whichparam' [-Wunused-parameter]
const long &whichparam) { assert(false); return 0;};
^
./src/postlike/plforces.h:468:44: warning: unused parameter 'param' [-Wunused-parameter]
double lnWait (const vector < double >¶m,
^
./src/postlike/plforces.h:469:40: warning: unused parameter 'treedata' [-Wunused-parameter]
const TreeSummary * treedata) { return 1.0; };
^
./src/postlike/plforces.h:471:45: warning: unused parameter 'param' [-Wunused-parameter]
double lnPoint (const vector < double >¶m,
^
./src/postlike/plforces.h:472:45: warning: unused parameter 'lparam' [-Wunused-parameter]
const vector < double >&lparam,
^
./src/postlike/plforces.h:473:41: warning: unused parameter 'treedata' [-Wunused-parameter]
const TreeSummary * treedata) { return 1.0; };
^
./src/postlike/plforces.h:475:45: warning: unused parameter 'param' [-Wunused-parameter]
double DlnWait (const vector < double >¶m,
^
./src/postlike/plforces.h:476:41: warning: unused parameter 'treedata' [-Wunused-parameter]
const TreeSummary * treedata,
^
./src/postlike/plforces.h:477:33: warning: unused parameter 'whichparam' [-Wunused-parameter]
const long &whichparam) { return 1.0; };
^
./src/postlike/plforces.h:479:46: warning: unused parameter 'param' [-Wunused-parameter]
double DlnPoint (const vector < double >¶m,
^
./src/postlike/plforces.h:480:42: warning: unused parameter 'treedata' [-Wunused-parameter]
const TreeSummary * treedata,
^
./src/postlike/plforces.h:481:34: warning: unused parameter 'whichparam' [-Wunused-parameter]
const long &whichparam) { return 1.0; };
^
In file included from src/bayeslike/bayesanalyzer_1d.cpp:26:
./src/force/force.h:256:61: warning: unused parameter 'fs' [-Wunused-parameter]
virtual void ModifyEvents(const ForceSummary& fs,
^
./src/force/force.h:549:61: warning: unused parameter 'mystatus' [-Wunused-parameter]
virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); };
^
./src/force/force.h:583:61: warning: unused parameter 'mystatus' [-Wunused-parameter]
virtual std::string MakeStatusXML(const std::string& mystatus) const { return string(""); };
^
72 warnings generated.
mv -f .deps/lamarc-bayesanalyzer_1d.Tpo .deps/lamarc-bayesanalyzer_1d.Po
c++ -DHAVE_CONFIG_H -I. -I./config -DLAMARC_COMPILE_LINUX -DNDEBUG -Wall -Wextra -Wno-unused -I ./config -I ./config -I ./src/bayeslike -I ./src/control -I ./src/conversion -I ./src/convErr -I ./src/convModel -I ./src/convParse -I ./src/convStrings -I ./src/convUtil -I ./src/datalike -I ./src/force -I ./src/guiconv -I ./src/guiutil -I ./src/lamarcmenus -I ./src/menu -I ./src/postlike -I ./src/report -I ./src/tools -I ./src/tree -I ./src/ui_interface -I ./src/ui_util -I ./src/ui_vars -I ./src/xml -I ./boost -I ./resources -I ./tinyxml -DTIXML_USE_STL -O2 -pipe -fno-strict-aliasing -MT lamarc-bayescurve.o -MD -MP -MF .deps/lamarc-bayescurve.Tpo -c -o lamarc-bayescurve.o `test -f 'src/bayeslike/bayescurve.cpp' || echo './'`src/bayeslike/bayescurve.cpp
In file included from src/bayeslike/bayescurve.cpp:31:
In file included from ./src/control/registry.h:22:
In file included from ./src/tools/random.h:15:
In file included from ./boost/random.hpp:42:
In file included from ./boost/random/ranlux.hpp:21:
./boost/random/discard_block.hpp:68:38: warning: unused parameter 'x' [-Wunused-parameter]
static bool validation(result_type x) { return true; } // dummy
^
In file included from src/bayeslike/bayescurve.cpp:31:
In file included from ./src/control/registry.h:22:
In file included from ./src/tools/random.h:15:
In file included from ./boost/random.hpp:53:
In file included from ./boost/random/random_number_generator.hpp:22:
In file included from ./boost/random/uniform_int.hpp:26:
./boost/random/uniform_smallint.hpp:39:63: warning: unused parameter 'ud' [-Wunused-parameter]
InputStream& extract_uniform_int(InputStream& is, UniformInt& ud, Impl& impl)
^
In file included from src/bayeslike/bayescurve.cpp:31:
In file included from ./src/control/registry.h:24:
In file included from ./src/control/regiongammainfo.h:16:
./src/force/paramstat.h:99:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:100:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_identical); };
^
./src/force/paramstat.h:121:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:122:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:163:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:164:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:181:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:182:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:201:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:202:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:219:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:220:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
14 warnings generated.
mv -f .deps/lamarc-bayescurve.Tpo .deps/lamarc-bayescurve.Po
c++ -DHAVE_CONFIG_H -I. -I./config -DLAMARC_COMPILE_LINUX -DNDEBUG -Wall -Wextra -Wno-unused -I ./config -I ./config -I ./src/bayeslike -I ./src/control -I ./src/conversion -I ./src/convErr -I ./src/convModel -I ./src/convParse -I ./src/convStrings -I ./src/convUtil -I ./src/datalike -I ./src/force -I ./src/guiconv -I ./src/guiutil -I ./src/lamarcmenus -I ./src/menu -I ./src/postlike -I ./src/report -I ./src/tools -I ./src/tree -I ./src/ui_interface -I ./src/ui_util -I ./src/ui_vars -I ./src/xml -I ./boost -I ./resources -I ./tinyxml -DTIXML_USE_STL -O2 -pipe -fno-strict-aliasing -MT lamarc-bayesparamlike_1d.o -MD -MP -MF .deps/lamarc-bayesparamlike_1d.Tpo -c -o lamarc-bayesparamlike_1d.o `test -f 'src/bayeslike/bayesparamlike_1d.cpp' || echo './'`src/bayeslike/bayesparamlike_1d.cpp
In file included from src/bayeslike/bayesparamlike_1d.cpp:18:
./src/control/defaults.h:286:18: error: unknown type name 'time_t'
static const time_t programstarttime;
^
In file included from src/bayeslike/bayesparamlike_1d.cpp:20:
In file included from ./src/tree/parameter.h:66:
./src/force/paramstat.h:99:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:100:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_identical); };
^
./src/force/paramstat.h:121:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:122:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:163:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:164:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:181:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:182:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:201:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:202:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
./src/force/paramstat.h:219:59: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleIndividualStatus(force_type ftype) const { return ToString(pstat_unconstrained); };
^
./src/force/paramstat.h:220:54: warning: unused parameter 'ftype' [-Wunused-parameter]
virtual std::string ToggleGroupStatus(force_type ftype) const { return ToString(pstat_constant); };
^
12 warnings and 1 error generated.
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/lamarc/work/lamarc-2.1.8
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/lamarc
===> Cleaning for lamarc-2.1.8,1
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