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Gentoo's Bugzilla – Attachment 447534 Details for
Bug 594904
sci-biology/cufflinks-2.2.1-r2 : ./.../error.h:70:27: error: return-statement with no value, in function returning ‘lemon::ExceptionMember<_Type>&’ [-fpermissive]
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sci-biology:cufflinks-2.2.1-r2:20160923-024601.log
sci-biology:cufflinks-2.2.1-r2:20160923-024601.log (text/plain), 73.81 KB, created by
Toralf Förster
on 2016-09-23 18:12:12 UTC
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Description:
sci-biology:cufflinks-2.2.1-r2:20160923-024601.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2016-09-23 18:12:12 UTC
Size:
73.81 KB
patch
obsolete
> * 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 â__m128 {aka __vector(4) float}â [-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 â__m128i {aka __vector(2) long long int}â [-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 â__m128d {aka __vector(2) double}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet4i {aka __vector(2) long long int}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet4i {aka __vector(2) long long int}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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: âtemplate<class _Operation> class std::binder2ndâ 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: âtemplate<class _Operation> class std::binder1stâ 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 âvoid 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*)â: >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:574:9: warning: this âifâ 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 âifâ > traits.initAcc(C4); > ^~~~~~ >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:946:9: warning: this âifâ 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 âifâ > traits.acc(C0, alphav, R0); > ^~~~~~ >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:951:9: warning: this âifâ 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 âifâ > 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 âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<float, 4, 1>, float, float, Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<float, 4, 1>â >/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16: required from âclass Eigen::Quaternion<float>â >/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 âEigen::internal::packet_traits<float>::type {aka __vector(4) float}â [-Wignored-attributes] > >::type PacketReturnType; > ^~~~~~~~~~~~~~~~ >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, 4, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<double, 4, 1>â >/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16: required from âclass Eigen::Quaternion<double>â >/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 âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-Wignored-attributes] >In file included from abundances.h:23:0, > from clustering.h:38, > from clustering.cpp:10: >hits.h: In constructor âPrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)â: >hits.h:928:12: warning: âPrecomputedExpressionHitFactory::_expression_file_nameâ will be initialized after [-Wreorder] > string _expression_file_name; > ^~~~~~~~~~~~~~~~~~~~~ >hits.h:927:19: warning: âstd::ifstream PrecomputedExpressionHitFactory::_ifsâ [-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 âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, -1, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<double, -1, 1>â >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:656:50: required from âstd::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]â >abundances.h:494:58: required from here >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-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 â__m128 {aka __vector(4) float}â [-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 â__m128i {aka __vector(2) long long int}â [-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 â__m128d {aka __vector(2) double}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet4i {aka __vector(2) long long int}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet4i {aka __vector(2) long long int}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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: âtemplate<class _Operation> class std::binder2ndâ 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: âtemplate<class _Operation> class std::binder1stâ 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 âvoid 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*)â: >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:574:9: warning: this âifâ 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 âifâ > traits.initAcc(C4); > ^~~~~~ >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:946:9: warning: this âifâ 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 âifâ > traits.acc(C0, alphav, R0); > ^~~~~~ >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:951:9: warning: this âifâ 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 âifâ > 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 âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<float, 4, 1>, float, float, Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<float, 4, 1>â >/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16: required from âclass Eigen::Quaternion<float>â >/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 âEigen::internal::packet_traits<float>::type {aka __vector(4) float}â [-Wignored-attributes] > >::type PacketReturnType; > ^~~~~~~~~~~~~~~~ >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, 4, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<double, 4, 1>â >/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16: required from âclass Eigen::Quaternion<double>â >/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 âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-Wignored-attributes] >In file included from abundances.h:23:0, > from differential.cpp:20: >hits.h: In constructor âPrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)â: >hits.h:928:12: warning: âPrecomputedExpressionHitFactory::_expression_file_nameâ will be initialized after [-Wreorder] > string _expression_file_name; > ^~~~~~~~~~~~~~~~~~~~~ >hits.h:927:19: warning: âstd::ifstream PrecomputedExpressionHitFactory::_ifsâ [-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 âdouble boost::numeric::ublas::cholesky_factorize(M&)â: >sampling.h:50:13: warning: typedef âmatrix_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef M matrix_type; > ^~~~~~~~~~~ >In file included from differential.cpp:24:0: >sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression<E2>&)â: >sampling.h:113:19: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef const M const_matrix_type; > ^~~~~~~~~~~~~~~~~ >sampling.h:114:42: warning: typedef âvector_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef vector<typename E::value_type> vector_type; > ^~~~~~~~~~~ >sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression<E2>&)â: >sampling.h:120:19: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef const M const_matrix_type; > ^~~~~~~~~~~~~~~~~ >sampling.h:121:42: warning: typedef âmatrix_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef matrix<typename E::value_type> matrix_type; > ^~~~~~~~~~~ >sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression<E>&, const M&)â: >sampling.h:127:19: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef const M const_matrix_type; > ^~~~~~~~~~~~~~~~~ >sampling.h:128:42: warning: typedef âvector_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef vector<typename E::value_type> vector_type; > ^~~~~~~~~~~ >sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression<E>&, const M&)â: >sampling.h:134:19: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] > typedef const M const_matrix_type; > ^~~~~~~~~~~~~~~~~ >sampling.h:135:42: warning: typedef âmatrix_typeâ 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 âvoid TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >)â: >differential.cpp:120:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] > assert (abundances.size() == _orig_workers); > ~~~~~~~~~~~~~~~~~~^~~~ >differential.cpp: In member function âvoid TestLauncher::record_tracking_data(std::vector<boost::shared_ptr<SampleAbundances> >&)â: >differential.cpp:148:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] > assert (abundances.size() == _orig_workers); > ~~~~~~~~~~~~~~~~~~^~~~ >differential.cpp: In function âSampleDifference test_diffexp(const FPKMContext&, const FPKMContext&)â: >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 âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, -1, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<double, -1, 1>â >differential.cpp:689:21: required from here >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-Wignored-attributes] > >::type PacketReturnType; > ^~~~~~~~~~~~~~~~ >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of âclass Eigen::DenseCoeffsBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >, 0>â: >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct 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>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> > >â >/usr/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h:49:7: required from âclass Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, Eigen::Matrix<double, -1, 1> >â >differential.cpp:689:91: required from here >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-Wignored-attributes] >differential.cpp: In function âbool test_js(const AbundanceGroup&, const AbundanceGroup&, double&, double&)â: >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 âclass Eigen::DenseCoeffsBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> >, 0>â: >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct 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>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> > >â >/usr/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h:92:7: required from âclass Eigen::CwiseUnaryOpImpl<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1>, Eigen::Dense>â >/usr/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h:59:7: required from âclass Eigen::CwiseUnaryOp<Eigen::internal::scalar_quotient1_op<double>, const Eigen::Matrix<double, -1, 1> >â >differential.cpp:743:131: required from here >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-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 âvoid test_differential(const string&, const std::vector<boost::shared_ptr<SampleAbundances> >&, const std::vector<std::pair<long unsigned int, long unsigned int> >&, Tests&, Tracking&)â: >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 âclass 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>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass 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>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass 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>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct 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>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass 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> > > >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass 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> > > >â >/usr/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:63: required from âclass 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> > >â >/usr/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:184:110: required from âDerived& Eigen::DenseBase<Derived>::operator/=(const Scalar&) [with Derived = Eigen::Matrix<double, -1, 1>; Eigen::DenseBase<Derived>::Scalar = double]â >differential.cpp:701:40: required from here >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-Wignored-attributes] > >::type PacketReturnType; > ^~~~~~~~~~~~~~~~ >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of âclass 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>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass 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>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass 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>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct 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>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass 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> > > >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass 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> > > >â >/usr/include/eigen3/Eigen/src/Core/SelfCwiseBinaryOp.h:45:63: required from âclass 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> > >â >/usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:223:77: required from âDerived& 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>]â >differential.cpp:743:131: required from here >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-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 âPrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)â: >hits.h:928:12: warning: âPrecomputedExpressionHitFactory::_expression_file_nameâ will be initialized after [-Wreorder] > string _expression_file_name; > ^~~~~~~~~~~~~~~~~~~~~ >hits.h:927:19: warning: âstd::ifstream PrecomputedExpressionHitFactory::_ifsâ [-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: âtemplate<class> class std::auto_ptrâ 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 âlemon::ExceptionMember<_Type>& lemon::ExceptionMember<_Type>::operator=(const lemon::ExceptionMember<_Type>&)â: >./lemon/error.h:70:27: error: return-statement with no value, in function returning âlemon::ExceptionMember<_Type>&â [-fpermissive] > if (ptr.get() == 0) return; > ^~~~~~ >./lemon/error.h:72:21: error: return-statement with no value, in function returning âlemon::ExceptionMember<_Type>&â [-fpermissive] > if (!copy.valid()) return; > ^~~~~~ >./lemon/error.h: At global scope: >./lemon/error.h:108:10: warning: âtemplate<class> class std::auto_ptrâ 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 âPrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)â: >hits.h:928:12: warning: âPrecomputedExpressionHitFactory::_expression_file_nameâ will be initialized after [-Wreorder] > string _expression_file_name; > ^~~~~~~~~~~~~~~~~~~~~ >hits.h:927:19: warning: âstd::ifstream PrecomputedExpressionHitFactory::_ifsâ [-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 â__m128 {aka __vector(4) float}â [-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 â__m128i {aka __vector(2) long long int}â [-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 â__m128d {aka __vector(2) double}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet4i {aka __vector(2) long long int}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet4i {aka __vector(2) long long int}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet4f {aka __vector(4) float}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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 âEigen::internal::Packet2d {aka __vector(2) double}â [-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: âtemplate<class _Operation> class std::binder2ndâ 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: âtemplate<class _Operation> class std::binder1stâ 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 âvoid 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*)â: >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:574:9: warning: this âifâ 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 âifâ > traits.initAcc(C4); > ^~~~~~ >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:946:9: warning: this âifâ 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 âifâ > traits.acc(C0, alphav, R0); > ^~~~~~ >/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:951:9: warning: this âifâ 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 âifâ > 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 âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<float, 4, 1>, float, float, Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<float, 4, 1>â >/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16: required from âclass Eigen::Quaternion<float>â >/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 âEigen::internal::packet_traits<float>::type {aka __vector(4) float}â [-Wignored-attributes] > >::type PacketReturnType; > ^~~~~~~~~~~~~~~~ >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, 4, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<double, 4, 1>â >/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:282:16: required from âclass Eigen::Quaternion<double>â >/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 âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-Wignored-attributes] >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 0>â: >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:274:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 1>â >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:636:7: required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>â >/usr/include/eigen3/Eigen/src/Core/util/XprHelper.h:371:8: required from âstruct Eigen::internal::special_scalar_op_base<Eigen::Matrix<double, -1, 1>, double, double, Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, 1>, 3>, false>â >/usr/include/eigen3/Eigen/src/Core/DenseBase.h:41:34: required from âclass Eigen::DenseBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/MatrixBase.h:48:34: required from âclass Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/PlainObjectBase.h:88:7: required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >â >/usr/include/eigen3/Eigen/src/Core/Matrix.h:127:7: required from âclass Eigen::Matrix<double, -1, 1>â >/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_vector.h:656:50: required from âstd::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]â >abundances.h:494:58: required from here >/usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument âEigen::internal::packet_traits<double>::type {aka __vector(2) double}â [-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'
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