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Date:      Tue, 19 Dec 2017 07:25:41 GMT
From:      pkg-fallout@FreeBSD.org
To:        scottcheloha@gmail.com
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - head-amd64-default][biology/bedtools] Failed for bedtools-2.25.0 in build
Message-ID:  <201712190725.vBJ7PfPo079355@beefy12.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 455167 2017-11-30 06:13:34Z linimon $
Log URL:        http://beefy12.nyi.freebsd.org/data/head-amd64-default/p456698_s326954/logs/bedtools-2.25.0.log
Build URL:      http://beefy12.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p456698_s326954
Log:

=>> Building biology/bedtools
build started at Tue Dec 19 07:23:52 UTC 2017
port directory: /usr/ports/biology/bedtools
package name: bedtools-2.25.0
building for: FreeBSD head-amd64-default-job-09 12.0-CURRENT FreeBSD 12.0-CURRENT 1200054 amd64
maintained by: scottcheloha@gmail.com
Makefile ident:      $FreeBSD: head/biology/bedtools/Makefile 455167 2017-11-30 06:13:34Z linimon $
Poudriere version: 3.2.3-16-g77e43413
Host OSVERSION: 1200052
Jail OSVERSION: 1200054
Job Id: 09




!!! Jail is newer than host. (Jail: 1200054, Host: 1200052) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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scottcheloha@gmail.com
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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
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#### /usr/local/etc/poudriere.d/make.conf ####
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=======================<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
[head-amd64-default-job-09] Installing pkg-1.10.3_1...
[head-amd64-default-job-09] 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
[head-amd64-default-job-09] Installing gmake-4.2.1_1...
[head-amd64-default-job-09] `-- Installing gettext-runtime-0.19.8.1_1...
[head-amd64-default-job-09] |   `-- Installing indexinfo-0.3.1...
[head-amd64-default-job-09] |   `-- Extracting indexinfo-0.3.1: .... done
[head-amd64-default-job-09] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[head-amd64-default-job-09] 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
[head-amd64-default-job-09] Installing python27-2.7.14_1...
[head-amd64-default-job-09] `-- Installing libffi-3.2.1_2...
[head-amd64-default-job-09] `-- Extracting libffi-3.2.1_2: .......... done
[head-amd64-default-job-09] `-- Installing readline-7.0.3_1...
[head-amd64-default-job-09] `-- Extracting readline-7.0.3_1: .......... done
[head-amd64-default-job-09] 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

<snip>
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
3 warnings generated.
  * compiling BedPlusInterval.cpp
In file included from BedPlusInterval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling Bed12Interval.cpp
In file included from Bed12Interval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling BamRecord.cpp
In file included from BamRecord.cpp:8:
In file included from ./BamRecord.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling GffRecord.cpp
In file included from GffRecord.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling GffPlusRecord.cpp
In file included from GffPlusRecord.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling VcfRecord.cpp
In file included from VcfRecord.cpp:9:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling NoPosPlusRecord.cpp
In file included from NoPosPlusRecord.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling BlockMgr.cpp
In file included from BlockMgr.cpp:9:
In file included from ./RecordMgr.h:21:
In file included from ./BamRecord.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
./../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]
const char GZIP_ID2   = 139;
           ~~~~~~~~     ^~~
./../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
           ~~~~~~~~~~   ^~~
2 warnings generated.
  * compiling StrandQueue.cpp
In file included from StrandQueue.cpp:8:
In file included from ./StrandQueue.h:11:
/usr/include/c++/v1/queue:401:5: error: static_assert failed ""
    static_assert((is_same<_Tp, value_type>::value), "" );
    ^             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/v1/__config:783:36: 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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