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Date:      Sat, 23 Dec 2017 20:33:06 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 111arm64-default][biology/bedtools] Failed for bedtools-2.25.0 in build
Message-ID:  <201712232033.vBNKX6UO001993@thunderx1.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:     scottcheloha@gmail.com
Last committer: linimon@FreeBSD.org
Ident:          $FreeBSD: head/biology/bedtools/Makefile 456719 2017-12-19 14:41:29Z linimon $
Log URL:        http://thunderx1.nyi.freebsd.org/data/111arm64-default/456912/logs/bedtools-2.25.0.log
Build URL:      http://thunderx1.nyi.freebsd.org/build.html?mastername=111arm64-default&build=456912
Log:

=>> Building biology/bedtools
build started at Sat Dec 23 20:24:40 UTC 2017
port directory: /usr/ports/biology/bedtools
package name: bedtools-2.25.0
building for: FreeBSD 111arm64-default-job-11 11.1-RELEASE-p6 FreeBSD 11.1-RELEASE-p6 1101001 arm64
maintained by: scottcheloha@gmail.com
Makefile ident:      $FreeBSD: head/biology/bedtools/Makefile 456719 2017-12-19 14:41:29Z linimon $
Poudriere version: 3.2.3-16-g77e43413
Host OSVERSION: 1200052
Jail OSVERSION: 1101001
Job Id: 11

---Begin Environment---
SHELL=/bin/csh
OSVERSION=1101001
UNAME_v=FreeBSD 11.1-RELEASE-p6 1101001
UNAME_r=11.1-RELEASE-p6
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/111arm64-default/ref
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
OLDPWD=/usr/local/poudriere/data/.m/111arm64-default/ref/.p
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
PWD=/usr/local/poudriere/data/.m/111arm64-default/ref/.p/pool
MASTERNAME=111arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
P_PYTHON_MAJOR_VER=2
POUDRIERE_VERSION=3.2.3-16-g77e43413
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
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--
scottcheloha@gmail.com
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work  HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bedtools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bedtools/work  HOME=/wrkdirs/usr/ports/biology/bedtools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bedtools/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  LIBDIR="/usr/lib"  CC="cc" CFLAGS="-O2 -pipe  -fno-strict-aliasing"  CPP="cpp" CPPFLAGS=""  LDFLAGS="" LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing "  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--
PYTHON_INCLUDEDIR=include/python2.7  PYTHON_LIBDIR=lib/python2.7  PYTHON_PLATFORM=freebsd11  PYTHON_PYOEXTENSION=pyo  PYTHON_SITELIBDIR=lib/python2.7/site-packages  PYTHON_SUFFIX=27  PYTHON_VER=2.7  PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/bedtools"  EXAMPLESDIR="share/examples/bedtools"  DATADIR="share/bedtools"  WWWDIR="www/bedtools"  ETCDIR="etc/bedtools"
--End PLIST_SUB--

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

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /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=aarch64
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=11.1
OSVERSION=1101001
PYTHONBASE=/usr/local
UID=0
_OSRELEASE=11.1-RELEASE-p6
#### Misc Poudriere ####
GID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  1048576
stack size              (kbytes, -s)  1048576
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 GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   bedtools-2.25.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.3_1.txz
[111arm64-default-job-11] Installing pkg-1.10.3_1...
[111arm64-default-job-11] Extracting pkg-1.10.3_1: .......... done
===>   bedtools-2.25.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of bedtools-2.25.0
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by bedtools-2.25.0 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by bedtools-2.25.0 for building
=> SHA256 Checksum OK for arq5x-bedtools2-v2.25.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by bedtools-2.25.0 for building
===>  Extracting for bedtools-2.25.0
=> SHA256 Checksum OK for arq5x-bedtools2-v2.25.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for bedtools-2.25.0
===>  Applying FreeBSD patches for bedtools-2.25.0
===========================================================================
=======================<phase: build-depends  >============================
===>   bedtools-2.25.0 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_1.txz
[111arm64-default-job-11] Installing gmake-4.2.1_1...
[111arm64-default-job-11] `-- Installing gettext-runtime-0.19.8.1_1...
[111arm64-default-job-11] |   `-- Installing indexinfo-0.3.1...
[111arm64-default-job-11] |   `-- Extracting indexinfo-0.3.1: .... done
[111arm64-default-job-11] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[111arm64-default-job-11] Extracting gmake-4.2.1_1: .......... done
===>   bedtools-2.25.0 depends on executable: gmake - found
===>   Returning to build of bedtools-2.25.0
===>   bedtools-2.25.0 depends on file: /usr/local/bin/python2.7 - not found
===>   Installing existing package /packages/All/python27-2.7.14_1.txz
[111arm64-default-job-11] Installing python27-2.7.14_1...
[111arm64-default-job-11] `-- Installing libffi-3.2.1_2...
[111arm64-default-job-11] `-- Extracting libffi-3.2.1_2: .......... done
[111arm64-default-job-11] `-- Installing readline-7.0.3_1...
[111arm64-default-job-11] `-- Extracting readline-7.0.3_1: .......... done
[111arm64-default-job-11] Extracting python27-2.7.14_1: .......... done
Message from python27-2.7.14_1:

===========================================================================

Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

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

===========================================================================
===>   bedtools-2.25.0 depends on file: /usr/local/bin/python2.7 - found
===>   Returning to build of bedtools-2.25.0
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for bedtools-2.25.0
===========================================================================
=======================<phase: build          >============================
===>  Building for bedtools-2.25.0
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.25.0'
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.25.0
CURRENT_VERSION  = 
Updating version file.
 * Creating BamTools API
- Building in src/utils/bedFile
  * compiling bedFile.cpp
- Building in src/utils/BinTree
  * compiling BinTree.cpp
BinTree.cpp:118:13: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if (binNum < 0 || binNum >= NUM_BINS) {
            ~~~~~~ ^ ~
In file included from BinTree.cpp:1:
./BinTree.h:69:13: warning: private field '_maxBinNumFound' is not used [-Wunused-private-field]
        binNumType _maxBinNumFound;
                   ^
2 warnings generated.
- Building in src/utils/version
  * compiling version.cpp
- Building in src/utils/bedGraphFile
  * compiling bedGraphFile.cpp
- Building in src/utils/chromsweep
  * compiling chromsweep.cpp
- Building in src/utils/Contexts
  * compiling ContextBase.cpp
  * compiling ContextIntersect.cpp
  * compiling ContextFisher.cpp
  * compiling ContextMap.cpp
  * compiling ContextSample.cpp
  * compiling ContextSpacing.cpp
  * compiling ContextMerge.cpp
  * compiling ContextJaccard.cpp
  * compiling ContextClosest.cpp
  * compiling ContextSubtract.cpp
  * compiling ContextCoverage.cpp
  * compiling ContextComplement.cpp
  * compiling ContextGroupBy.cpp
- Building in src/utils/FileRecordTools
  * compiling FileRecordMgr.cpp
  * compiling FileRecordMergeMgr.cpp
- Building in FileReaders
  * compiling FileReader.cpp
  * compiling SingleLineDelimTextFileReader.cpp
  * compiling BamFileReader.cpp
  * compiling BufferedStreamMgr.cpp
  * compiling InputStreamMgr.cpp
- Building in Records
  * compiling Record.cpp
  * compiling EmptyRecord.cpp
  * compiling Bed3Interval.cpp
  * compiling Bed4Interval.cpp
  * compiling BedGraphInterval.cpp
  * compiling Bed5Interval.cpp
  * compiling Bed6Interval.cpp
  * compiling PlusFields.cpp
In file included from PlusFields.cpp:1:
./PlusFields.h:11:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
  * compiling BedPlusInterval.cpp
  * compiling Bed12Interval.cpp
  * compiling BamRecord.cpp
  * compiling GffRecord.cpp
  * compiling GffPlusRecord.cpp
  * compiling VcfRecord.cpp
  * compiling NoPosPlusRecord.cpp
  * compiling BlockMgr.cpp
  * compiling StrandQueue.cpp
In file included from StrandQueue.cpp:8:
In file included from ./StrandQueue.h:11:
/usr/include/c++/v1/queue:405:5: error: static_assert failed ""
    static_assert((is_same<_Tp, value_type>::value), "" );
    ^             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/v1/__config:727:36: note: expanded from macro 'static_assert'
#   define static_assert(__b, __m) _Static_assert(__b, __m)
                                   ^              ~~~
StrandQueue.cpp:13:26: note: in instantiation of template class 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>' requested here
                queueType *queue = new queueType();
                                       ^
StrandQueue.cpp:32:47: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
        return const_cast<Record *>(_queues[minIdx]->top());
                                    ~~~~~~~~~~~~~~~  ^
StrandQueue.cpp:38:19: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
        _queues[minIdx]->pop();
        ~~~~~~~~~~~~~~~  ^
StrandQueue.cpp:45:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                if (_queues[0]->empty()) return NULL;
                    ~~~~~~~~~~  ^
StrandQueue.cpp:46:24: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                record = _queues[0]->top();
                         ~~~~~~~~~~  ^
StrandQueue.cpp:49:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                if (_queues[1]->empty()) return NULL;
                    ~~~~~~~~~~  ^
StrandQueue.cpp:51:24: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                record = _queues[1]->top();
                         ~~~~~~~~~~  ^
StrandQueue.cpp:54:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                if (_queues[0]->empty()) return NULL;
                    ~~~~~~~~~~  ^
StrandQueue.cpp:55:24: error: no member named 'top' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                record = _queues[2]->top();
                         ~~~~~~~~~~  ^
StrandQueue.cpp:66:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                if (_queues[0]->empty()) return;
                    ~~~~~~~~~~  ^
StrandQueue.cpp:67:15: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                _queues[0]->pop();
                ~~~~~~~~~~  ^
StrandQueue.cpp:70:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                if (_queues[1]->empty()) return;
                    ~~~~~~~~~~  ^
StrandQueue.cpp:71:15: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                _queues[1]->pop();
                ~~~~~~~~~~  ^
StrandQueue.cpp:74:19: error: no member named 'empty' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                if (_queues[2]->empty()) return;
                    ~~~~~~~~~~  ^
StrandQueue.cpp:75:15: error: no member named 'pop' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                _queues[2]->pop();
                ~~~~~~~~~~  ^
StrandQueue.cpp:85:15: error: no member named 'push' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                _queues[0]->push(record);
                ~~~~~~~~~~  ^
StrandQueue.cpp:88:15: error: no member named 'push' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                _queues[1]->push(record);
                ~~~~~~~~~~  ^
StrandQueue.cpp:91:15: error: no member named 'push' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                _queues[2]->push(record);
                ~~~~~~~~~~  ^
StrandQueue.cpp:101:26: error: no member named 'size' in 'std::__1::priority_queue<Record *, std::__1::vector<const Record *, std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
                sumSize += _queues[i]->size();
                           ~~~~~~~~~~  ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake[3]: *** [Makefile:39: ../../../../obj//StrandQueue.o] Error 1
gmake[2]: *** [Makefile:45: Records] Error 2
gmake[1]: *** [Makefile:174: src/utils/FileRecordTools] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bedtools/work/bedtools2-2.25.0'
*** Error code 1

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



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