[package - head-amd64-default][biology/bedtools] Failed for bedtools-2.25.0 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Jul 8 03:28:02 UTC 2017
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 at gmail.com
Last committer: linimon at FreeBSD.org
Ident: $FreeBSD: head/biology/bedtools/Makefile 441847 2017-05-27 15:07:11Z linimon $
Log URL: http://beefy12.nyi.freebsd.org/data/head-amd64-default/p445290_s320796/logs/bedtools-2.25.0.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p445290_s320796
Log:
====>> Building biology/bedtools
build started at Sat Jul 8 03:26:05 UTC 2017
port directory: /usr/ports/biology/bedtools
building for: FreeBSD head-amd64-default-job-23 12.0-CURRENT FreeBSD 12.0-CURRENT 1200037 amd64
maintained by: scottcheloha at gmail.com
Makefile ident: $FreeBSD: head/biology/bedtools/Makefile 441847 2017-05-27 15:07:11Z linimon $
Poudriere version: 3.1.19-47-g9ae57ef8
Host OSVERSION: 1200033
Jail OSVERSION: 1200037
Job Id: 23
!!! Jail is newer than host. (Jail: 1200037, Host: 1200033) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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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" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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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-1.10.1.txz
[head-amd64-default-job-23] Installing pkg-1.10.1...
[head-amd64-default-job-23] Extracting pkg-1.10.1: .......... 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-23] Installing gmake-4.2.1_1...
[head-amd64-default-job-23] `-- Installing gettext-runtime-0.19.8.1_1...
[head-amd64-default-job-23] | `-- Installing indexinfo-0.2.6...
[head-amd64-default-job-23] | `-- Extracting indexinfo-0.2.6: .... done
[head-amd64-default-job-23] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[head-amd64-default-job-23] Extracting gmake-4.2.1_1: .......... done
===> bedtools-2.25.0 depends on executable: gmake - found
<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: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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