* Package:    sci-biology/cufflinks-2.2.1-r2
 * Repository: gentoo
 * Maintainer: sci-biology@gentoo.org
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking cufflinks-2.2.1.tar.gz to /var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work
>>> Preparing source in /var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1 ...
 * Applying cufflinks-2.2.1-samtools-legacy.patch ...
 [ ok ]
 * Applying cufflinks-2.2.1-flags.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1' ...
 * Running aclocal ...
 [ ok ]
 * Running autoconf --force ...
 [ ok ]
 * Running autoheader ...
 [ ok ]
 * Running automake --add-missing --copy --foreign --force-missing ...
 [ ok ]
 * Running elibtoolize in: cufflinks-2.2.1/
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1 ...
 * econf: updating cufflinks-2.2.1/build-aux/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating cufflinks-2.2.1/build-aux/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/cufflinks-2.2.1-r2 --htmldir=/usr/share/doc/cufflinks-2.2.1-r2/html --libdir=/usr/lib64 --disable-optim --with-boost-libdir=/usr/lib64/ --with-bam=/usr/ --disable-debug
checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) gawk
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-g++... none
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking whether make sets $(MAKE)... (cached) yes
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking the archiver (x86_64-pc-linux-gnu-ar) interface... ar
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 3.4
checking for python platform... linux
checking for python script directory... ${prefix}/lib64/python3.4/site-packages
checking for python extension module directory... ${exec_prefix}/lib64/python3.4/site-packages
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking build system type... x86_64-pc-linux-gnu
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system-mt... yes
checking for exit in -lboost_system-mt... (cached) yes
checking whether the Boost::Serialization library is available... yes
checking for exit in -lboost_serialization-mt... yes
checking for exit in -lboost_serialization-mt... (cached) yes
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-mt... yes
checking for exit in -lboost_system-mt... (cached) yes
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for eigenlib... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... x86_64-pc-linux-gnu
checking if gcc accepts -m64... yes
checking for struct sysinfo.totalram... yes
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of x86_64-pc-linux-gnu-gcc... (cached) none
checking dependency style of x86_64-pc-linux-gnu-g++... (cached) none
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands

-- cufflinks 2.2.1 Configuration Results --
  C++ compiler:        x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -Wunused -Wuninitialized -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed
  GCC version:         x86_64-pc-linux-gnu-gcc (Gentoo 6.2.0-r1 p1.1) 6.2.0
  Host System type:    x86_64-pc-linux-gnu
  Install prefix:      /usr
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <cole@cs.umd.edu> with questions and bug reports.

>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1 ...
make -j1 
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1'
Making all in src
make[2]: Entering directory '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1/src'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..  -I../src  -I/usr/include/eigen3 -I/usr/include -pthread -I/usr/include -I/usr//include   -Wall -Wno-strict-aliasing -Wunused -Wuninitialized -march=native -O2 -pipe -c -o clustering.o clustering.cpp
In file included from /usr/include/eigen3/Eigen/Core:263:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:29:39: warning: ignoring attributes on template argument ‘__m128 {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128>  { enum { value = true }; };
                                       ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:30:40: warning: ignoring attributes on template argument ‘__m128i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128i> { enum { value = true }; };
                                        ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:31:40: warning: ignoring attributes on template argument ‘__m128d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128d> { enum { value = true }; };
                                        ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:101:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4}; };
                                           ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:102:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2}; };
                                           ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:103:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4}; };
                                           ^
In file included from /usr/include/eigen3/Eigen/Core:263:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:519:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4f>
                                   ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:529:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4i>
                                   ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:539:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet2d>
                                   ^
In file included from /usr/include/eigen3/Eigen/Core:265:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:211:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet4f, Packet2cf, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:220:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet2cf, Packet4f, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:407:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet2d, Packet1cd, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:416:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet1cd, Packet2d, false,false>
                                                               ^
In file included from /usr/include/eigen3/Eigen/Core:276:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^~~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_function.h:1127:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:48,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/locale_classes.h:40,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ios_base.h:41,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ios:42,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:38,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iterator:64,
                 from /usr/include/boost/iterator.hpp:10,
                 from /usr/include/boost/graph/vector_as_graph.hpp:21,
                 from clustering.h:17,
                 from clustering.cpp:10:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:276:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^~~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_function.h:1127:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/string:48,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/locale_classes.h:40,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/ios_base.h:41,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ios:42,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/ostream:38,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iterator:64,
                 from /usr/include/boost/iterator.hpp:10,
                 from /usr/include/boost/graph/vector_as_graph.hpp:21,
                 from clustering.h:17,
                 from clustering.cpp:10:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/binders.h:108:11: note: declared here
     class binder1st
           ^~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:326:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In member function ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar*, Index, const LhsScalar*, const RhsScalar*, Index, Index, Index, Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index, RhsScalar*)’:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:574:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) traits.initAcc(C3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:575:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   traits.initAcc(C4);
                   ^~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:946:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) R3 = ploadu<ResPacket>(r3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:948:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   traits.acc(C0, alphav, R0);
                   ^~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:951:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) traits.acc(C3, alphav, R3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:953:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   pstoreu(r0, R0);
                   ^~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:277:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<float, 4, 1>, float, float, Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<float, 4, 1>’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16:   required from ‘class Eigen::Quaternion<float>’
/usr/include/eigen3/Eigen/src/Geometry/arch/Geometry_SSE.h:22:3:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, 4, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<double, 4, 1>’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16:   required from ‘class Eigen::Quaternion<double>’
/usr/include/eigen3/Eigen/src/Geometry/arch/Geometry_SSE.h:63:3:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
In file included from abundances.h:23:0,
                 from clustering.h:38,
                 from clustering.cpp:10:
hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’:
hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder]
     string _expression_file_name;
            ^~~~~~~~~~~~~~~~~~~~~
hits.h:927:19: warning:   ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder]
     std::ifstream _ifs;
                   ^~~~
In file included from abundances.h:23:0,
                 from clustering.h:38,
                 from clustering.cpp:10:
hits.h:814:5: warning:   when initialized here [-Wreorder]
     PrecomputedExpressionHitFactory(const string& expression_file_name,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:277:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from clustering.cpp:10:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, -1, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<double, -1, 1>’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:656:50:   required from ‘std::vector<_Tp, _Alloc>::size_type std::vector<_Tp, _Alloc>::size() const [with _Tp = Eigen::Matrix<double, -1, 1>; _Alloc = std::allocator<Eigen::Matrix<double, -1, 1> >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’
abundances.h:494:58:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..  -I../src  -I/usr/include/eigen3 -I/usr/include -pthread -I/usr/include -I/usr//include   -Wall -Wno-strict-aliasing -Wunused -Wuninitialized -march=native -O2 -pipe -c -o differential.o differential.cpp
In file included from /usr/include/eigen3/Eigen/Core:263:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:29:39: warning: ignoring attributes on template argument ‘__m128 {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128>  { enum { value = true }; };
                                       ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:30:40: warning: ignoring attributes on template argument ‘__m128i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128i> { enum { value = true }; };
                                        ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:31:40: warning: ignoring attributes on template argument ‘__m128d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128d> { enum { value = true }; };
                                        ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:101:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4}; };
                                           ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:102:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2}; };
                                           ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:103:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4}; };
                                           ^
In file included from /usr/include/eigen3/Eigen/Core:263:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:519:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4f>
                                   ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:529:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4i>
                                   ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:539:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet2d>
                                   ^
In file included from /usr/include/eigen3/Eigen/Core:265:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:211:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet4f, Packet2cf, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:220:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet2cf, Packet4f, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:407:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet2d, Packet1cd, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:416:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet1cd, Packet2d, false,false>
                                                               ^
In file included from /usr/include/eigen3/Eigen/Core:276:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^~~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_function.h:1127:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/functional:49,
                 from differential.cpp:11:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:276:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^~~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_function.h:1127:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/functional:49,
                 from differential.cpp:11:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/binders.h:108:11: note: declared here
     class binder1st
           ^~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:326:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In member function ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar*, Index, const LhsScalar*, const RhsScalar*, Index, Index, Index, Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index, RhsScalar*)’:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:574:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) traits.initAcc(C3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:575:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   traits.initAcc(C4);
                   ^~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:946:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) R3 = ploadu<ResPacket>(r3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:948:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   traits.acc(C0, alphav, R0);
                   ^~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:951:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) traits.acc(C3, alphav, R3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:953:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   pstoreu(r0, R0);
                   ^~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:277:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<float, 4, 1>, float, float, Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<float, 4, 1>’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16:   required from ‘class Eigen::Quaternion<float>’
/usr/include/eigen3/Eigen/src/Geometry/arch/Geometry_SSE.h:22:3:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, 4, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<double, 4, 1>’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16:   required from ‘class Eigen::Quaternion<double>’
/usr/include/eigen3/Eigen/src/Geometry/arch/Geometry_SSE.h:63:3:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
In file included from abundances.h:23:0,
                 from differential.cpp:20:
hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’:
hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder]
     string _expression_file_name;
            ^~~~~~~~~~~~~~~~~~~~~
hits.h:927:19: warning:   ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder]
     std::ifstream _ifs;
                   ^~~~
In file included from abundances.h:23:0,
                 from differential.cpp:20:
hits.h:814:5: warning:   when initialized here [-Wreorder]
     PrecomputedExpressionHitFactory(const string& expression_file_name,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from differential.cpp:24:0:
sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&)’:
sampling.h:50:13: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef M matrix_type;
             ^~~~~~~~~~~
In file included from differential.cpp:24:0:
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression<E2>&)’:
sampling.h:113:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef const M const_matrix_type;
                   ^~~~~~~~~~~~~~~~~
sampling.h:114:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef vector<typename E::value_type> vector_type;
                                          ^~~~~~~~~~~
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression<E2>&)’:
sampling.h:120:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef const M const_matrix_type;
                   ^~~~~~~~~~~~~~~~~
sampling.h:121:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef matrix<typename E::value_type> matrix_type;
                                          ^~~~~~~~~~~
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression<E>&, const M&)’:
sampling.h:127:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef const M const_matrix_type;
                   ^~~~~~~~~~~~~~~~~
sampling.h:128:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef vector<typename E::value_type> vector_type;
                                          ^~~~~~~~~~~
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression<E>&, const M&)’:
sampling.h:134:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef const M const_matrix_type;
                   ^~~~~~~~~~~~~~~~~
sampling.h:135:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
   typedef matrix<typename E::value_type> matrix_type;
                                          ^~~~~~~~~~~
In file included from /usr/include/boost/assert.hpp:58:0,
                 from /usr/include/boost/smart_ptr/shared_array.hpp:21,
                 from /usr/include/boost/shared_array.hpp:17,
                 from /usr/include/boost/graph/detail/d_ary_heap.hpp:20,
                 from /usr/include/boost/graph/named_function_params.hpp:24,
                 from /usr/include/boost/graph/depth_first_search.hpp:21,
                 from clustering.h:20,
                 from differential.cpp:22:
differential.cpp: In member function ‘void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >)’:
differential.cpp:120:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     assert (abundances.size() == _orig_workers);
             ~~~~~~~~~~~~~~~~~~^~~~
differential.cpp: In member function ‘void TestLauncher::record_tracking_data(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:148:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     assert (abundances.size() == _orig_workers);
             ~~~~~~~~~~~~~~~~~~^~~~
differential.cpp: In function ‘SampleDifference test_diffexp(const FPKMContext&, const FPKMContext&)’:
differential.cpp:460:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size())
                                             ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:468:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size())
                                             ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:490:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size())
                                             ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:498:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size())
                                             ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:277:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, -1, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<double, -1, 1>’
differential.cpp:689:21:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >, 0>’:
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >, double, double, Eigen::DenseCoeffsBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >, 0>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >’
/usr/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:49:7:   required from ‘class Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >’
differential.cpp:689:91:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
differential.cpp: In function ‘bool test_js(const AbundanceGroup&, const AbundanceGroup&, double&, double&)’:
differential.cpp:742:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size())
                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:277:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> >, 0>’:
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> >, double, double, Eigen::DenseCoeffsBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> >, 0>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >’
/usr/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h:92:7:   required from ‘class Eigen::CwiseUnaryOpImpl<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1>, Eigen::Dense>’
/usr/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h:59:7:   required from ‘class Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> >’
differential.cpp:743:131:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
differential.cpp:754:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size())
                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:780:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size())
                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:792:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size())
                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
differential.cpp: In function ‘void test_differential(const string&, const std::vector<boost::shared_ptr<SampleAbundances> >&, const std::vector<std::pair<long unsigned int, long unsigned int> >&, Tests&, Tracking&)’:
differential.cpp:1506:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test &&
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:1507:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                           prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test);
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:1545:77: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     bool enough_reads =  (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test &&
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:1546:77: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                           prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test);
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:1583:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test &&
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
differential.cpp:1584:76: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                           prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test);
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:277:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from differential.cpp:20:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >, double, double, Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > > >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > > >’
/usr/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:63:   required from ‘class Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >’
/usr/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:184:110:   required from ‘Derived& Eigen::DenseBase<Derived>::operator/=(const Scalar&) [with Derived = Eigen::Matrix<double, -1, 1>; Eigen::DenseBase<Derived>::Scalar = double]’
differential.cpp:701:40:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >, double, double, Eigen::DenseCoeffsBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > > >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > > >’
/usr/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:63:   required from ‘class Eigen::SelfCwiseBinaryOp<Eigen::internal::scalar_sum_op<double>, Eigen::Matrix<double, -1, 1>, Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >’
/usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:223:77:   required from ‘Derived& Eigen::MatrixBase<Derived>::operator+=(const Eigen::MatrixBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> >; Derived = Eigen::Matrix<double, -1, 1>]’
differential.cpp:743:131:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..  -I../src  -I/usr/include/eigen3 -I/usr/include -pthread -I/usr/include -I/usr//include   -Wall -Wno-strict-aliasing -Wunused -Wuninitialized -march=native -O2 -pipe -c -o common.o common.cpp
In file included from bundles.h:20:0,
                 from replicates.h:10,
                 from common.cpp:28:
hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’:
hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder]
     string _expression_file_name;
            ^~~~~~~~~~~~~~~~~~~~~
hits.h:927:19: warning:   ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder]
     std::ifstream _ifs;
                   ^~~~
In file included from bundles.h:20:0,
                 from replicates.h:10,
                 from common.cpp:28:
hits.h:814:5: warning:   when initialized here [-Wreorder]
     PrecomputedExpressionHitFactory(const string& expression_file_name,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..  -I../src  -I/usr/include/eigen3 -I/usr/include -pthread -I/usr/include -I/usr//include   -Wall -Wno-strict-aliasing -Wunused -Wuninitialized -march=native -O2 -pipe -c -o assemble.o assemble.cpp
In file included from ./lemon/bits/base_extender.h:23:0,
                 from ./lemon/list_graph.h:26,
                 from ./lemon/dfs.h:26,
                 from ./lemon/topology.h:22,
                 from assemble.cpp:19:
./lemon/error.h:93:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     std::auto_ptr<_Type> ptr;
          ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from ./lemon/error.h:31,
                 from ./lemon/bits/base_extender.h:23,
                 from ./lemon/list_graph.h:26,
                 from ./lemon/dfs.h:26,
                 from ./lemon/topology.h:22,
                 from assemble.cpp:19:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from ./lemon/bits/base_extender.h:23:0,
                 from ./lemon/list_graph.h:26,
                 from ./lemon/dfs.h:26,
                 from ./lemon/topology.h:22,
                 from assemble.cpp:19:
./lemon/error.h: In member function ‘lemon::ExceptionMember<_Type>& lemon::ExceptionMember<_Type>::operator=(const lemon::ExceptionMember<_Type>&)’:
./lemon/error.h:70:27: error: return-statement with no value, in function returning ‘lemon::ExceptionMember<_Type>&’ [-fpermissive]
       if (ptr.get() == 0) return;
                           ^~~~~~
./lemon/error.h:72:21: error: return-statement with no value, in function returning ‘lemon::ExceptionMember<_Type>&’ [-fpermissive]
  if (!copy.valid()) return;
                     ^~~~~~
./lemon/error.h: At global scope:
./lemon/error.h:108:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     std::auto_ptr<std::ostringstream> buf;
          ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from ./lemon/error.h:31,
                 from ./lemon/bits/base_extender.h:23,
                 from ./lemon/list_graph.h:26,
                 from ./lemon/dfs.h:26,
                 from ./lemon/topology.h:22,
                 from assemble.cpp:19:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from bundles.h:20:0,
                 from assemble.h:21,
                 from assemble.cpp:48:
hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’:
hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder]
     string _expression_file_name;
            ^~~~~~~~~~~~~~~~~~~~~
hits.h:927:19: warning:   ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder]
     std::ifstream _ifs;
                   ^~~~
In file included from bundles.h:20:0,
                 from assemble.h:21,
                 from assemble.cpp:48:
hits.h:814:5: warning:   when initialized here [-Wreorder]
     PrecomputedExpressionHitFactory(const string& expression_file_name,
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:263:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from assemble.cpp:54:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h: At global scope:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:29:39: warning: ignoring attributes on template argument ‘__m128 {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128>  { enum { value = true }; };
                                       ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:30:40: warning: ignoring attributes on template argument ‘__m128i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128i> { enum { value = true }; };
                                        ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:31:40: warning: ignoring attributes on template argument ‘__m128d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128d> { enum { value = true }; };
                                        ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:101:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4}; };
                                           ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:102:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2}; };
                                           ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:103:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4}; };
                                           ^
In file included from /usr/include/eigen3/Eigen/Core:263:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from assemble.cpp:54:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:519:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4f>
                                   ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:529:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4i>
                                   ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/PacketMath.h:539:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet2d>
                                   ^
In file included from /usr/include/eigen3/Eigen/Core:265:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from assemble.cpp:54:
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:211:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet4f, Packet2cf, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:220:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet2cf, Packet4f, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:407:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet2d, Packet1cd, false,false>
                                                               ^
/usr/include/eigen3/Eigen/src/Core/arch/SSE/Complex.h:416:63: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct conj_helper<Packet1cd, Packet2d, false,false>
                                                               ^
In file included from /usr/include/eigen3/Eigen/Core:276:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from assemble.cpp:54:
/usr/include/eigen3/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^~~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_function.h:1127:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_tree.h:65,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/map:60,
                 from assemble.cpp:14:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:276:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from assemble.cpp:54:
/usr/include/eigen3/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^~~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_function.h:1127:0,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_tree.h:65,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/map:60,
                 from assemble.cpp:14:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/backward/binders.h:108:11: note: declared here
     class binder1st
           ^~~~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:326:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from assemble.cpp:54:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In member function ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar*, Index, const LhsScalar*, const RhsScalar*, Index, Index, Index, Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index, RhsScalar*)’:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:574:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) traits.initAcc(C3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:575:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   traits.initAcc(C4);
                   ^~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:946:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) R3 = ploadu<ResPacket>(r3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:948:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   traits.acc(C0, alphav, R0);
                   ^~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:951:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if(nr==4) traits.acc(C3, alphav, R3);
         ^~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:953:19: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                   pstoreu(r0, R0);
                   ^~~~~~~
In file included from /usr/include/eigen3/Eigen/Core:277:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from abundances.h:21,
                 from clustering.h:38,
                 from assemble.cpp:54:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<float, 4, 1>, float, float, Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<float, 4, 1>’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16:   required from ‘class Eigen::Quaternion<float>’
/usr/include/eigen3/Eigen/src/Geometry/arch/Geometry_SSE.h:22:3:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, 4, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<double, 4, 1>’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16:   required from ‘class Eigen::Quaternion<double>’
/usr/include/eigen3/Eigen/src/Geometry/arch/Geometry_SSE.h:63:3:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 0>’:
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 1>’
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>’
/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8:   required from ‘struct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, -1, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>, false>’
/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >’
/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7:   required from ‘class Eigen::Matrix<double, -1, 1>’
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:656:50:   required from ‘std::vector<_Tp, _Alloc>::size_type std::vector<_Tp, _Alloc>::size() const [with _Tp = Eigen::Matrix<double, -1, 1>; _Alloc = std::allocator<Eigen::Matrix<double, -1, 1> >; std::vector<_Tp, _Alloc>::size_type = long unsigned int]’
abundances.h:494:58:   required from here
/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
make[2]: *** [Makefile:1626: assemble.o] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1/src'
make[1]: *** [Makefile:400: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1'
make: *** [Makefile:341: all] Error 2
 * ERROR: sci-biology/cufflinks-2.2.1-r2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/cufflinks-2.2.1-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/cufflinks-2.2.1-r2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:cufflinks-2.2.1-r2:20160923-024601.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1'
 * S: '/var/tmp/portage/sci-biology/cufflinks-2.2.1-r2/work/cufflinks-2.2.1'