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Date:      Fri, 15 Aug 2014 15:57:04 GMT
From:      pkg-fallout@FreeBSD.org
To:        mzaki@m.u-tokyo.ac.jp
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - head-amd64-default][biology/mrbayes] Failed for mrbayes-3.1.2_1 in build
Message-ID:  <201408151557.s7FFv4iH020243@beefy2.isc.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:     mzaki@m.u-tokyo.ac.jp
Last committer: mat@FreeBSD.org
Ident:          $FreeBSD: head/biology/mrbayes/Makefile 340722 2014-01-22 17:00:46Z mat $
Log URL:        http://beefy2.isc.freebsd.org/data/head-amd64-default/2014-08-14_16h56m28s/logs/mrbayes-3.1.2_1.log
Build URL:      http://beefy2.isc.freebsd.org/build.html?mastername=head-amd64-default&build=2014-08-14_16h56m28s
Log:

====>> Building biology/mrbayes
build started at Fri Aug 15 15:56:35 UTC 2014
port directory: /usr/ports/biology/mrbayes
building for: FreeBSD head-amd64-default-job-05 11.0-CURRENT FreeBSD 11.0-CURRENT r269901 amd64
maintained by: mzaki@m.u-tokyo.ac.jp
Makefile ident:      $FreeBSD: head/biology/mrbayes/Makefile 340722 2014-01-22 17:00:46Z mat $
Poudriere version: 3.1-pre
Host OSVERSION: 1100027
Jail OSVERSION: 1100028




!!! Jail is newer than host. (Jail: 1100028, Host: 1100027) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
OSVERSION=1100028
UNAME_v=FreeBSD 11.0-CURRENT r269901
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=screen
MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=mrbayes-3.1.2_1
OLDPWD=/root/poudriere
PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool
MASTERNAME=head-amd64-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---End Environment---

---Begin OPTIONS List---
===> The following configuration options are available for mrbayes-3.1.2_1:
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mrbayes/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work  HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" MAKE=gmake SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mrbayes/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work  HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" NO_PIE=yes 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="-I/usr/local/include"  LDFLAGS=" -L/usr/local/lib" LIBS=""  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--

--PLIST_SUB--
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
PORTDATA=""
LIB32DIR=lib
DOCSDIR="share/doc/mrbayes"
EXAMPLESDIR="share/examples/mrbayes"
DATADIR="share/mrbayes"
WWWDIR="www/mrbayes"
ETCDIR="etc/mrbayes"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/mrbayes
DOCSDIR=/usr/local/share/doc/mrbayes
EXAMPLESDIR=/usr/local/share/examples/mrbayes
WWWDIR=/usr/local/www/mrbayes
ETCDIR=/usr/local/etc/mrbayes
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
# clean-restricted ran via poudriere.conf NO_RESTRICTED
#NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
=======================<phase: check-sanity   >============================
===========================================================================
=======================<phase: pkg-depends    >============================
===>   mrbayes-3.1.2_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-1.3.6.txz
[head-amd64-default-job-05] Installing pkg-1.3.6... done
Message for pkg-1.3.6:
 If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of mrbayes-3.1.2_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===> Fetching all distfiles required by mrbayes-3.1.2_1 for building
===========================================================================
=======================<phase: checksum       >============================
===> Fetching all distfiles required by mrbayes-3.1.2_1 for building
=> SHA256 Checksum OK for mrbayes-3.1.2.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===> Fetching all distfiles required by mrbayes-3.1.2_1 for building
===>  Extracting for mrbayes-3.1.2_1
=> SHA256 Checksum OK for mrbayes-3.1.2.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for mrbayes-3.1.2_1
===>  Applying FreeBSD patches for mrbayes-3.1.2_1
===========================================================================
=======================<phase: build-depends  >============================
===>   mrbayes-3.1.2_1 depends on executable: gmake - not found
===>    Verifying install for gmake in /usr/ports/devel/gmake
===>   Installing existing package /packages/All/gmake-3.82_1.txz
[head-amd64-default-job-05] Installing indexinfo-0.2... done
[head-amd64-default-job-05] Installing indexinfo-0.2... done
[head-amd64-default-job-05] Installing indexinfo-0.2... done
===>   Returning to build of mrbayes-3.1.2_1
===========================================================================
=======================<phase: lib-depends    >============================
===>   mrbayes-3.1.2_1 depends on shared library: libreadline.so.6 - not found
===>    Verifying for libreadline.so.6 in /usr/ports/devel/readline
===>   Installing existing package /packages/All/readline-6.3.6_1.txz
[head-amd64-default-job-05] Installing readline-6.3.6_1... done
===>   Returning to build of mrbayes-3.1.2_1
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for mrbayes-3.1.2_1
===========================================================================
=======================<phase: build          >============================
===>  Building for mrbayes-3.1.2_1
gmake[1]: Entering directory `/wrkdirs/usr/ports/biology/mrbayes/work/mrbayes-3.1.2'
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o mb.o mb.c
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o mcmc.o mcmc.c
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o bayes.o bayes.c
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o command.o command.c
command.c:1371:12: warning: variable 'tempD' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                else if (calibrationPtr->prior == offsetExponential)
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
command.c:1403:25: note: uninitialized use occurs here
                sprintf (s, "%1.2lf", tempD);
                                      ^~~~~
command.c:1371:8: note: remove the 'if' if its condition is always true
                else if (calibrationPtr->prior == offsetExponential)
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
command.c:1227:16: note: initialize the variable 'tempD' to silence this warning
        MrBFlt                  tempD;
                                     ^
                                      = 0.0
command.c:7813:3: warning: expression result unused [-Wunused-value]
                *tokenP++;
                ^~~~~~~~~
2 warnings generated.
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o mbmath.o mbmath.c
mbmath.c:4788:5: warning: use of unary operator that may be intended as compound assignment (-=)
                r =- log(RandomNumber(seed));
                  ^~
1 warning generated.
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o model.o model.c
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o plot.o plot.c
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o sump.o sump.c
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall  -I/usr/local/include  -c -o sumt.o sumt.c
cc -O2 -pipe  -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall   mb.o bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o   -lncurses -lreadline  -lm -o mb
/usr/bin/ld: cannot find -lreadline
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [mb] Error 1
gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/mrbayes/work/mrbayes-3.1.2'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/mrbayes



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