[package - 121armv7-quarterly][biology/star] Failed for rna-STAR-2.7.3.a in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Dec 1 02:20:19 UTC 2020
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: jwb at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: branches/2020Q4/biology/star/Makefile 531206 2020-04-09 12:43:03Z jwb $
Log URL: http://beefy13.nyi.freebsd.org/data/121armv7-quarterly/556693/logs/rna-STAR-2.7.3.a.log
Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=121armv7-quarterly&build=556693
Log:
=>> Building biology/star
build started at Tue Dec 1 02:06:12 UTC 2020
port directory: /usr/ports/biology/star
package name: rna-STAR-2.7.3.a
building for: FreeBSD 121armv7-quarterly-job-14 12.1-RELEASE-p10 FreeBSD 12.1-RELEASE-p10 1201000 arm
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q4/biology/star/Makefile 531206 2020-04-09 12:43:03Z jwb $
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> rna-STAR-2.7.3.a depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.10.txz
[121armv7-quarterly-job-14] Installing pkg-1.15.10...
[121armv7-quarterly-job-14] Extracting pkg-1.15.10: .......... done
===> rna-STAR-2.7.3.a depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rna-STAR-2.7.3.a
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.3.a for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.3.a for building
=> SHA256 Checksum OK for alexdobin-STAR-2.7.3a_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by rna-STAR-2.7.3.a for building
===> Extracting for rna-STAR-2.7.3.a
=> SHA256 Checksum OK for alexdobin-STAR-2.7.3a_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
<snip>
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
In file included from /usr/local/lib/gcc9/include/c++/bits/stl_algo.h:61,
from /usr/local/lib/gcc9/include/c++/algorithm:62,
from IncludeDefine.h:5,
from SoloBarcode.h:3,
from SoloBarcode.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/local/lib/gcc9/include/c++/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/algorithm:62,
from IncludeDefine.h:5,
from SoloBarcode.h:3,
from SoloBarcode.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h: In member function 'void SoloBarcode::sortWhiteList()':
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 ParametersSolo.cpp
In file included from /usr/local/lib/gcc9/include/c++/vector:72,
from IncludeDefine.h:14,
from ParametersSolo.h:6,
from ParametersSolo.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/algorithm:62,
from IncludeDefine.h:5,
from ParametersSolo.h:6,
from ParametersSolo.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
In file included from /usr/local/lib/gcc9/include/c++/bits/stl_algo.h:61,
from /usr/local/lib/gcc9/include/c++/algorithm:62,
from IncludeDefine.h:5,
from ParametersSolo.h:6,
from ParametersSolo.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/local/lib/gcc9/include/c++/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/algorithm:62,
from IncludeDefine.h:5,
from ParametersSolo.h:6,
from ParametersSolo.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/vector:67,
from IncludeDefine.h:14,
from ParametersSolo.h:6,
from ParametersSolo.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_vector.h: In member function 'void ParametersSolo::initialize(Parameters*)':
/usr/local/lib/gcc9/include/c++/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/algorithm:62,
from IncludeDefine.h:5,
from ParametersSolo.h:6,
from ParametersSolo.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/vector:67,
from IncludeDefine.h:14,
from ParametersSolo.h:6,
from ParametersSolo.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloRead.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloRead_record.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadBarcode.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadBarcode_getCBandUMI.cpp
In file included from /usr/local/lib/gcc9/include/c++/vector:72,
from IncludeDefine.h:14,
from SoloReadBarcode.h:4,
from SoloReadBarcode_getCBandUMI.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/local/lib/gcc9/include/c++/vector:67,
from IncludeDefine.h:14,
from SoloReadBarcode.h:4,
from SoloReadBarcode_getCBandUMI.cpp:1:
/usr/local/lib/gcc9/include/c++/bits/stl_vector.h: In member function 'void SoloReadBarcode::matchCBtoWL(std::string&, std::string&, std::vector<long long unsigned int>&, int&, std::vector<long long unsigned int>&, std::string&)':
/usr/local/lib/gcc9/include/c++/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloBarcode_extractBarcode.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadFeature.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadFeature_record.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadFeature_inputRecords.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 Solo.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature_collapseUMI.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature_outputResults.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature_processRecords.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature_addBAMtags.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 ReadAlign_outputAlignments.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 ReadAlign.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 STAR.cpp
In file included from /usr/local/lib/gcc9/include/c++/vector:72,
from IncludeDefine.h:14,
from STAR.cpp:4:
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SharedMemory.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 PackedArray.cpp
g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 1 02:13:47 UTC 2020 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SuffixArrayFuns.cpp
In file included from SuffixArrayFuns.h:4,
from SuffixArrayFuns.cpp:1:
SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)':
IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean '__uint32_t'?
58 | #define uint128 __uint128_t
| ^~~~~~~~~~~
SuffixArrayFuns.cpp:362:18: note: in expansion of macro 'uint128'
362 | register uint128 g1=*( (uint128*) (gSeq+SAstr) );
| ^~~~~~~
SuffixArrayFuns.cpp:365:37: error: 'g1' was not declared in this scope; did you mean 'g2'?
365 | register char g2=(char) g1;
| ^~
| g2
In file included from SuffixArrayFuns.h:4,
from SuffixArrayFuns.cpp:1:
IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean '__uint32_t'?
58 | #define uint128 __uint128_t
| ^~~~~~~~~~~
SuffixArrayFuns.cpp:379:18: note: in expansion of macro 'uint128'
379 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) );
| ^~~~~~~
SuffixArrayFuns.cpp:382:38: error: 'g1' was not declared in this scope; did you mean 'g2'?
382 | register char g2=(char) (g1>>(8*(15-ii)));
| ^~
| g2
SuffixArrayFuns.cpp:353:29: warning: unused parameter 'gSeq' [-Wunused-parameter]
353 | uint funCalcSAiFromSA(char* gSeq, PackedArray& gSA, Genome &mapGen, uint iSA, int L, int & iL4)
| ~~~~~~^~~~
gmake[1]: *** [Makefile:69: SuffixArrayFuns.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.3a/source'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/star
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