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:     h2+fbsdpo...@fsfe.org
Last committer: ger...@freebsd.org
Ident:          $FreeBSD: head/biology/seqan/Makefile 347809 2014-03-10 
20:55:20Z gerald $
Log URL:        
http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-05-16_11h58m06s/logs/seqan-1.3.1_2.log
Build URL:      
http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-05-16_11h58m06s
Log:

====>> Building biology/seqan
build started at Sat May 17 04:39:24 UTC 2014
port directory: /usr/ports/biology/seqan
building for: FreeBSD head-amd64-default-job-11 11.0-CURRENT FreeBSD 
11.0-CURRENT r264257 amd64
maintained by: h2+fbsdpo...@fsfe.org
Makefile ident:      $FreeBSD: head/biology/seqan/Makefile 347809 2014-03-10 
20:55:20Z gerald $
Poudriere version: 3.1-pre
Host OSVERSION: 1100013
Jail OSVERSION: 1100018




!!! Jail is newer than host. (Jail: 1100018, Host: 1100013) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
OSVERSION=1100018
UNAME_v=FreeBSD 11.0-CURRENT r264257
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/build/head-amd64-default/ref
PKG_EXT=txz
tpid=638
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNG=1
PKGNAME=seqan-1.3.1_2
PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f
PKG_ADD=/usr/local/sbin/pkg-static add
OLDPWD=/usr/local/poudriere/data/build/head-amd64-default/ref/poudriere/rdeps
PWD=/usr/local/poudriere/data/build/head-amd64-default/ref/poudriere/pool
MASTERNAME=head-amd64-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
PKG_VERSION=/poudriere/pkg-static version
PKG_BIN=/usr/local/sbin/pkg-static
---End Environment---

---Begin OPTIONS List---
---End OPTIONS List---

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
TMPDIR="/tmp" PYTHON="/usr/local/bin/python2.7" TMPDIR="/tmp" SHELL=/bin/sh 
CONFIG_SHELL=/bin/sh
--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--

--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python2.7
PYTHON_LIBDIR=lib/python2.7
PYTHON_PLATFORM=freebsd11
PYTHON_SITELIBDIR=lib/python2.7/site-packages
PYTHON_VERSION=python2.7
CMAKE_BUILD_TYPE="release"
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
PORTDATA=""
LIB32DIR=lib
DOCSDIR="share/doc/seqan"
EXAMPLESDIR="share/examples/seqan"
DATADIR="share/seqan"
WWWDIR="www/seqan"
ETCDIR="etc/seqan"
--End PLIST_SUB--

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

---Begin make.conf---
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
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
===>  Cleaning for seqan-1.3.1_2
=======================<phase: check-sanity   >============================
===>  License BSD GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   seqan-1.3.1_2 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-1.2.7_2.txz
Installing pkg-1.2.7_2... done
If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of seqan-1.3.1_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-1.3.1_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-1.3.1_2 for building
=> SHA256 Checksum OK for seqan-1.3.1.zip.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License BSD GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-1.3.1_2 for building
===>  Extracting for seqan-1.3.1_2
=> SHA256 Checksum OK for seqan-1.3.1.zip.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for seqan-1.3.1_2
===>  Applying FreeBSD patches for seqan-1.3.1_2
===========================================================================
=======================<phase: build-depends  >============================
===>   seqan-1.3.1_2 depends on file: /usr/local/bin/python2.7 - not found
===>    Verifying install for /usr/local/bin/python2.7 in 
/usr/ports/lang/python27
===>   Installing existing package /packages/All/python27-2.7.6_4.txz
Installing python27-2.7.6_4...Installing gettext-0.18.3.1_1... done
 done
====
Note that some of the standard modules are provided as separate
ports since they require extra dependencies:

bsddb           databases/py-bsddb
gdbm            databases/py-gdbm
sqlite3         databases/py-sqlite3
tkinter         x11-toolkits/py-tkinter

Install them as needed.
====
===>   Returning to build of seqan-1.3.1_2
===>   seqan-1.3.1_2 depends on file: /usr/local/bin/cmake - not found
===>    Verifying install for /usr/local/bin/cmake in /usr/ports/devel/cmake
===>   Installing existing package /packages/All/cmake-2.8.12.1_4.txz
Installing cmake-2.8.12.1_4...Installing cmake-modules-2.8.12.1_1... done
 done
===>   Returning to build of seqan-1.3.1_2
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for seqan-1.3.1_2
===>  Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/seqan/work/.build
-- The C compiler identification is Clang 3.4.0
-- The CXX compiler identification is Clang 3.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PythonInterp: /usr/local/bin/python2.7 (found suitable version 
"2.7.6", minimum required is "2.7") 
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
<snip>
Linking C static library libbam.a
cd /wrkdirs/usr/ports/biology/seqan/work/.build/libs/samtools && 
/usr/local/bin/cmake -P CMakeFiles/bam.dir/cmake_clean_target.cmake
cd /wrkdirs/usr/ports/biology/seqan/work/.build/libs/samtools && 
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/bam.dir/link.txt 
--verbose=1
/usr/bin/ar cr libbam.a  CMakeFiles/bam.dir/bgzf.c.o 
CMakeFiles/bam.dir/kstring.c.o CMakeFiles/bam.dir/bam_aux.c.o 
CMakeFiles/bam.dir/bam.c.o CMakeFiles/bam.dir/bam_import.c.o 
CMakeFiles/bam.dir/sam.c.o CMakeFiles/bam.dir/bam_index.c.o 
CMakeFiles/bam.dir/bam_pileup.c.o CMakeFiles/bam.dir/bam_lpileup.c.o 
CMakeFiles/bam.dir/bam_md.c.o CMakeFiles/bam.dir/glf.c.o 
CMakeFiles/bam.dir/razf.c.o CMakeFiles/bam.dir/faidx.c.o 
CMakeFiles/bam.dir/knetfile.c.o CMakeFiles/bam.dir/bam_sort.c.o 
CMakeFiles/bam.dir/sam_header.c.o CMakeFiles/bam.dir/bam_reheader.c.o 
CMakeFiles/bam.dir/kprobaln.c.o
/usr/bin/ranlib libbam.a
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles  5 6 7 8 9 10 11 12 13 
14 15 16 17
[ 13%] Built target bam
/usr/bin/make -f CMakeFiles/Seqan.dir/build.make CMakeFiles/Seqan.dir/depend
cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E 
cmake_depends "Unix Makefiles" 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake 
/wrkdirs/usr/ports/biology/seqan/work/.build 
/wrkdirs/usr/ports/biology/seqan/work/.build 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles/Seqan.dir/DependInfo.cmake
Scanning dependencies of target Seqan
/usr/bin/make -f CMakeFiles/Seqan.dir/build.make CMakeFiles/Seqan.dir/build
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles
[ 13%] Built target Seqan
/usr/bin/make -f apps/CMakeFiles/dfi.dir/build.make 
apps/CMakeFiles/dfi.dir/depend
cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E 
cmake_depends "Unix Makefiles" 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/dfi.dir/DependInfo.cmake
Scanning dependencies of target dfi
/usr/bin/make -f apps/CMakeFiles/dfi.dir/build.make 
apps/CMakeFiles/dfi.dir/build
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 18
[ 14%] Building CXX object 
apps/CMakeFiles/dfi.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp.o
cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++    -O2 
-pipe -fno-strict-aliasing  -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 
-pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o 
CMakeFiles/dfi.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp.o
 -c /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:26:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/misc/misc_cmdparser.h:37:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/map.h:42:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9:
 warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header 
guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9:
 note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did 
you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
#define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:27:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:74:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78:
 warning: for loop has empty body [-Wempty-body]
                for(TSize _xSize = 1; _xSize <= saSize; _xSize *= BlockSize, 
++treeLevels) ;
                                                                                
           ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78:
 note: put the semicolon on a separate line to silence this warning
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:27:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:96:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54:
 warning: for loop has empty body [-Wempty-body]
                for(; lcpSize > _xSize; _xSize *= 2, ++treeLevels) ;
                                                                   ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54:
 note: put the semicolon on a separate line to silence this warning
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp:27:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:155:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49:
 warning: for loop has empty body [-Wempty-body]
                        for(_xSize = 1; _xSize < size; _xSize <<= 1) ;
                                                                     ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49:
 note: put the semicolon on a separate line to silence this warning
4 warnings generated.
Linking CXX executable dfi
cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/local/bin/cmake -E 
cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1
/usr/bin/c++   -O2 -pipe -fno-strict-aliasing  -DSEQAN_HAS_SAMTOOLS=1 
-DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0  
 
CMakeFiles/dfi.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/dfi/dfi.cpp.o
  -o dfi  -L/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib  -lz 
-Wl,-rpath,/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib: 
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles  18
[ 14%] Built target dfi
/usr/bin/make -f apps/CMakeFiles/insegt.dir/build.make 
apps/CMakeFiles/insegt.dir/depend
cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E 
cmake_depends "Unix Makefiles" 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/insegt.dir/DependInfo.cmake
Scanning dependencies of target insegt
/usr/bin/make -f apps/CMakeFiles/insegt.dir/build.make 
apps/CMakeFiles/insegt.dir/build
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 
[ 14%] Building CXX object 
apps/CMakeFiles/insegt.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp.o
cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++    -O2 
-pipe -fno-strict-aliasing  -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 
-pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o 
CMakeFiles/insegt.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp.o
 -c /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp:13:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9:
 warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header 
guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9:
 note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did 
you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
#define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
1 warning generated.
Linking CXX executable insegt
cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/local/bin/cmake -E 
cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1
/usr/bin/c++   -O2 -pipe -fno-strict-aliasing  -DSEQAN_HAS_SAMTOOLS=1 
-DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0  
 
CMakeFiles/insegt.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/insegt/insegt.cpp.o
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-Wl,-rpath,/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib: 
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles
[ 14%] Built target insegt
/usr/bin/make -f apps/CMakeFiles/mason.dir/build.make 
apps/CMakeFiles/mason.dir/depend
cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E 
cmake_depends "Unix Makefiles" 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/mason.dir/DependInfo.cmake
Scanning dependencies of target mason
/usr/bin/make -f apps/CMakeFiles/mason.dir/build.make 
apps/CMakeFiles/mason.dir/build
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 
[ 14%] Building CXX object 
apps/CMakeFiles/mason.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp.o
cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++    -O2 
-pipe -fno-strict-aliasing  -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 
-pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o 
CMakeFiles/mason.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp.o
 -c /wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp:44:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/find.h:43:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9:
 warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header 
guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9:
 note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did 
you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
#define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
1 warning generated.
Linking CXX executable mason
cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/local/bin/cmake -E 
cmake_link_script CMakeFiles/mason.dir/link.txt --verbose=1
/usr/bin/c++   -O2 -pipe -fno-strict-aliasing  -DSEQAN_HAS_SAMTOOLS=1 
-DSEQAN_ENABLE_TESTING=0 -O2 -pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0  
 
CMakeFiles/mason.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/mason/mason.cpp.o
  -o mason  -L/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib  -lz 
-Wl,-rpath,/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib: 
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles
[ 14%] Built target mason
/usr/bin/make -f apps/CMakeFiles/micro_razers.dir/build.make 
apps/CMakeFiles/micro_razers.dir/depend
cd /wrkdirs/usr/ports/biology/seqan/work/.build && /usr/local/bin/cmake -E 
cmake_depends "Unix Makefiles" 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/cmake/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps 
/wrkdirs/usr/ports/biology/seqan/work/.build/apps/CMakeFiles/micro_razers.dir/DependInfo.cmake
Scanning dependencies of target micro_razers
/usr/bin/make -f apps/CMakeFiles/micro_razers.dir/build.make 
apps/CMakeFiles/micro_razers.dir/build
/usr/local/bin/cmake -E cmake_progress_report 
/wrkdirs/usr/ports/biology/seqan/work/.build/CMakeFiles 47
[ 15%] Building CXX object 
apps/CMakeFiles/micro_razers.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp.o
cd /wrkdirs/usr/ports/biology/seqan/work/.build/apps && /usr/bin/c++    -O2 
-pipe -fno-strict-aliasing  -DSEQAN_HAS_SAMTOOLS=1 -DSEQAN_ENABLE_TESTING=0 -O2 
-pipe -fno-strict-aliasing -DSEQAN_ENABLE_DEBUG=0 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/lib/samtools 
-I/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1 -o 
CMakeFiles/micro_razers.dir/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp.o
 -c 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:28:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/find.h:43:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:103:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:38:9:
 warning: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header 
guard here, followed by #define of a different macro [-Wheader-guard]
#ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence/string_set_dependent_generous.h:39:9:
 note: 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did 
you mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
#define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:29:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:74:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78:
 warning: for loop has empty body [-Wempty-body]
                for(TSize _xSize = 1; _xSize <= saSize; _xSize *= BlockSize, 
++treeLevels) ;
                                                                                
           ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_sa_btree.h:119:78:
 note: put the semicolon on a separate line to silence this warning
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:29:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:96:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54:
 warning: for loop has empty body [-Wempty-body]
                for(; lcpSize > _xSize; _xSize *= 2, ++treeLevels) ;
                                                                   ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/index_lcp_tree.h:164:54:
 note: put the semicolon on a separate line to silence this warning
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:29:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index.h:155:
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49:
 warning: for loop has empty body [-Wempty-body]
                        for(_xSize = 1; _xSize < size; _xSize <<= 1) ;
                                                                     ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_index_esa.h:159:49:
 note: put the semicolon on a separate line to silence this warning
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:37:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:28:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/find.h:43:
In file included from 
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/sequence.h:54:
/usr/include/c++/v1/map:457:17: error: no matching function for call to object 
of type 'const seqan::RepeatLess_<unsigned int>'
        {return static_cast<const _Compare&>(*this)(__x.__cc.first, 
__y.__cc.first);}
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/v1/__tree:1613:17: note: in instantiation of member function 
'std::__1::__map_value_compare<unsigned int, std::__1::__value_type<unsigned 
int, seqan::Repeat<unsigned int, unsigned int> >, seqan::RepeatLess_<unsigned 
int>, true>::operator()' requested here
            if (value_comp()(__v, __nd->__value_))
                ^
/usr/include/c++/v1/__tree:1867:36: note: in instantiation of function template 
specialization 'std::__1::__tree<std::__1::__value_type<unsigned int, 
seqan::Repeat<unsigned int, unsigned int> >, 
std::__1::__map_value_compare<unsigned int, std::__1::__value_type<unsigned 
int, seqan::Repeat<unsigned int, unsigned int> >, seqan::RepeatLess_<unsigned 
int>, true>, std::__1::allocator<std::__1::__value_type<unsigned int, 
seqan::Repeat<unsigned int, unsigned int> > > 
>::__find_equal<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned 
int, unsigned int> > >' requested here
    __node_base_pointer& __child = __find_equal(__parent, __v);
                                   ^
/usr/include/c++/v1/map:1043:55: note: in instantiation of member function 
'std::__1::__tree<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned 
int, unsigned int> >, std::__1::__map_value_compare<unsigned int, 
std::__1::__value_type<unsigned int, seqan::Repeat<unsigned int, unsigned int> 
>, seqan::RepeatLess_<unsigned int>, true>, 
std::__1::allocator<std::__1::__value_type<unsigned int, seqan::Repeat<unsigned 
int, unsigned int> > > >::__insert_unique' requested here
        insert(const value_type& __v) {return __tree_.__insert_unique(__v);}
                                                      ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/repeat_base.h:290:13:
 note: in instantiation of member function 'std::__1::map<unsigned int, 
seqan::Repeat<unsigned int, unsigned int>, seqan::RepeatLess_<unsigned int>, 
std::__1::allocator<std::__1::pair<const unsigned int, seqan::Repeat<unsigned 
int, unsigned int> > > >::insert' requested here
                                                        
list.insert(::std::pair<TOcc,TRepeat>(rep.beginPosition, rep));
                                                             ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/find_swift.h:270:4:
 note: in instantiation of function template specialization 
'seqan::findRepeats<seqan::String<seqan::Repeat<unsigned int, unsigned int>, 
seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, 
seqan::Dna5_>, seqan::Alloc<void> >, int, int>' requested here
                        findRepeats(data_repeats, haystack, minRepeatLen, 
maxPeriod);
                        ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:1614:15:
 note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to 
see all)
        TSwiftFinder swiftFinder(genome, options.repeatLength, 1);
                     ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:1976:5:
 note: in instantiation of function template specialization 
'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> 
>, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, 
seqan::Alloc<void> >, 
seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, 
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > 
>, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, 
seqan::Dna_>, seqan::UngappedShape<0> >, const seqan::Tag<seqan::Default_> > >, 
seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_> >, 
seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
 char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, 
seqan::Myers<seqan::FindInfix, seqan::True, void> >, seqan::Alloc<void> >, 
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, 
seqan::Alloc<void> >, seqan
 ::RazerSSpec<false, false> >' requested here
                                mapSingleReads(matches, genome, gseqNo, 
swiftPattern, forwardPatterns, cnts, 'F', options);
                                ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:2133:10:
 note: in instantiation of function template specialization 
'seqan::mapSingleReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> 
>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, 
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > 
>, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, 
seqan::Alloc<void> >, seqan::RazerSSpec<false, false>, 
seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, 
seqan::UngappedShape<0> >, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_> 
> >' requested here
                return mapSingleReads(matches, genomeFileNameList, genomeNames, 
gnoToFileMap, readSet, cnts, options, shape, Swift<TSwiftSpec>());
                       ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/../razers/razers.h:2192:11:
 note: in instantiation of function template specialization 
'seqan::mapReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >, 
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, 
seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, 
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, 
seqan::Alloc<void> >, seqan::RazerSSpec<false, false>, 
seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, 
seqan::UngappedShape<0> >, seqan::Tag<seqan::SwiftSemiGlobal_<seqan::Hamming_> 
> >' requested here
                        return mapReads(matches, genomeFileNameList, 
genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, 
Swift<SwiftSemiGlobalHamming>());
                               ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:165:14:
 note: in instantiation of function template specialization 
'seqan::mapReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >, 
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, 
seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, 
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, 
seqan::Alloc<void> >, seqan::RazerSSpec<false, false> >' requested here
        int error = mapReads(matches, genomeFileNameList, genomeNames, 
gnoToFileMap, readSet, stats, options);
                    ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/apps/micro_razers/micro_razers.cpp:660:15:
 note: in instantiation of function template specialization 
'mapMicroRNAReads<seqan::RazerSSpec<false, false> >' requested here
        int result = mapMicroRNAReads(fname[0], fname + 1, 
errorPrbFileName.c_str(), options);
                     ^
/wrkdirs/usr/ports/biology/seqan/work/seqan-1.3.1/seqan/index/repeat_base.h:97:15:
 note: candidate function not viable: 'this' argument has type 'const 
seqan::RepeatLess_<unsigned int>', but method is not marked const
                inline bool operator() (TPos const &a, TPos const &b) {
                            ^
4 warnings and 1 error generated.
*** Error code 1

Stop.
make[3]: stopped in /wrkdirs/usr/ports/biology/seqan/work/.build
*** Error code 1

Stop.
make[2]: stopped in /wrkdirs/usr/ports/biology/seqan/work/.build
*** Error code 1

Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/seqan/work/.build
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/seqan
===>  Cleaning for seqan-1.3.1_2
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