--- Begin Message ---
Package: src:r-cran-seuratobject
Version: 5.3.0-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202602/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:r-cran-seuratobject, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules binary
dh binary --buildsystem R
dh_update_autotools_config -O--buildsystem=R
dh_autoreconf -O--buildsystem=R
dh_auto_configure -O--buildsystem=R
dh_auto_build -O--buildsystem=R
dh_auto_test -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=R
dh_prep -O--buildsystem=R
[... snipped ...]
27 | {
| ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<float>::typeâ {aka â__m128â}
[-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In
instantiation of âstruct Eigen::internal::find_best_packet<double, 4>â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:
required from âstruct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >â
22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar;
| ^~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49:
required from âstruct Eigen::internal::traits<Eigen::Quaternion<double>
>â
266 | Alignment = internal::traits<Coefficients>::Alignment,
| ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47:
required from here
98 | ResAlignment = traits<Quaternion<double> >::Alignment
| ^~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
190 | bool Stop = Size==Dynamic ||
(Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename
unpacket_traits<PacketType>::half>::value>
|
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
190 | bool Stop = Size==Dynamic ||
(Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename
unpacket_traits<PacketType>::half>::value>
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83:
warning: ignoring attributes on template argument
âEigen::internal::unpacket_traits<__vector(2) double>::halfâ {aka
â__m128dâ} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename
packet_traits<T>::type>::type type;
|
^~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In
instantiation of âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>,
0>â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7:
required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>,
1>â
302 | class DenseCoeffsBase<Derived, WriteAccessors> : public
DenseCoeffsBase<Derived, ReadOnlyAccessors>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7:
required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>,
3>â
555 | class DenseCoeffsBase<Derived, DirectWriteAccessors>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:
required from âclass Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >â
41 | template<typename Derived> class DenseBase
| ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:
required from âclass Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >â
48 | template<typename Derived> class MatrixBase
| ^~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:
required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1>
>â
98 | class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
| ^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:
required from âclass Eigen::Matrix<double, 4, 1>â
178 | class Matrix
| ^~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:
required from âclass Eigen::QuaternionBase<Eigen::Quaternion<double> >â
46 | typedef typename Coefficients::CoeffReturnType CoeffReturnType;
| ^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7:
required from âclass Eigen::Quaternion<double>â
273 | class Quaternion : public QuaternionBase<Quaternion<_Scalar,_Options> >
| ^~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3:
required from here
102 | {
| ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
In file included from
/usr/lib/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /usr/lib/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from
/usr/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:29:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:
In instantiation of âclass
Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:
required from âclass
Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >â
36 | class SparseCompressedBase
| ^~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7:
required from âclass Eigen::SparseMatrix<double, 0, int>â
96 | class SparseMatrix
| ^~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25:
required from here
61 | typedef Triplet<double> T;
| ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
47 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:
In instantiation of âclass
Eigen::SparseMatrixBase<Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> >
>â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:
required from âclass
Eigen::SparseCompressedBase<Eigen::Transpose<Eigen::SparseMatrix<double, 0,
int> > >â
36 | class SparseCompressedBase
| ^~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:22:9:
required from âclass
Eigen::internal::SparseTransposeImpl<Eigen::SparseMatrix<double, 0, int>,
1024>â
22 | class SparseTransposeImpl<MatrixType,CompressedAccessBit>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:45:37:
required from âclass Eigen::TransposeImpl<Eigen::SparseMatrix<double, 0,
int>, Eigen::Sparse>â
45 | template<typename MatrixType> class TransposeImpl<MatrixType,Sparse>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37:
required from âclass Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> >â
52 | template<typename MatrixType> class Transpose
| ^~~~~~~~~
data_manipulation.cpp:27:22: required from here
27 | mat = mat.transpose();
| ~~~~~~~~~~~~~^~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
47 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In
instantiation of âstruct Eigen::internal::find_best_packet<double, -1>â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:
required from âstruct Eigen::internal::traits<Eigen::Matrix<double, -1, -1>
>â
22 | typedef typename find_best_packet<_Scalar,size>::type PacketScalar;
| ^~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:
required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, -1, -1>
>â
98 | class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
| ^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:
required from âclass Eigen::Matrix<double, -1, -1>â
178 | class Matrix
| ^~~~~~
data_manipulation.cpp:33:26: required from here
33 | Eigen::MatrixXd nn_idx(mat.rows(), n);
| ^~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
190 | bool Stop = Size==Dynamic ||
(Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename
unpacket_traits<PacketType>::half>::value>
|
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
190 | bool Stop = Size==Dynamic ||
(Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename
unpacket_traits<PacketType>::half>::value>
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83:
warning: ignoring attributes on template argument
âEigen::internal::unpacket_traits<__vector(2) double>::halfâ {aka
â__m128dâ} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename
packet_traits<T>::type>::type type;
|
^~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In
instantiation of âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>,
0>â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7:
required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>,
1>â
302 | class DenseCoeffsBase<Derived, WriteAccessors> : public
DenseCoeffsBase<Derived, ReadOnlyAccessors>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7:
required from âclass Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>,
3>â
555 | class DenseCoeffsBase<Derived, DirectWriteAccessors>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:
required from âclass Eigen::DenseBase<Eigen::Matrix<double, -1, -1> >â
41 | template<typename Derived> class DenseBase
| ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:
required from âclass Eigen::MatrixBase<Eigen::Matrix<double, -1, -1> >â
48 | template<typename Derived> class MatrixBase
| ^~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:
required from âclass Eigen::PlainObjectBase<Eigen::Matrix<double, -1, -1>
>â
98 | class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
| ^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:
required from âclass Eigen::Matrix<double, -1, -1>â
178 | class Matrix
| ^~~~~~
data_manipulation.cpp:33:26: required from here
33 | Eigen::MatrixXd nn_idx(mat.rows(), n);
| ^~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:
In instantiation of âclass
Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 1, int> >â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:
required from âclass
Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 1, int> >â
36 | class SparseCompressedBase
| ^~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7:
required from âclass Eigen::SparseMatrix<double, 1, int>â
96 | class SparseMatrix
| ^~~~~~~~~~~~
data_manipulation.cpp:83:80: required from here
83 | mat_vec.emplace_back(Rcpp::as<Eigen::SparseMatrix<double,
Eigen::RowMajor>>(mat_list.at(i)));
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
47 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In
instantiation of âclass Eigen::DenseCoeffsBase<Eigen::SparseMatrix<double, 0,
int>, 0>â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80:
required from âstruct
Eigen::internal::evaluator<Eigen::SparseCompressedBase<Eigen::SparseMatrix<double,
0, int> > >â
336 | typedef typename
DenseCoeffsBase<Derived,ReadOnlyAccessors>::CoeffReturnType CoeffReturnType;
|
^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8:
required from âstruct
Eigen::internal::evaluator<Eigen::SparseMatrix<double, 0, int> >â
1505 | struct evaluator<SparseMatrix<_Scalar,_Options,_StorageIndex> >
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:58:63:
required from âstruct
Eigen::internal::unary_evaluator<Eigen::Transpose<Eigen::SparseMatrix<double,
0, int> >, Eigen::internal::IteratorBased, double>â
58 | typedef typename evaluator<ArgType>::InnerIterator
EvalIterator;
|
^~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:90:8:
required from âstruct
Eigen::internal::evaluator<Eigen::Transpose<Eigen::SparseMatrix<double, 0, int>
> >â
90 | struct evaluator : public unary_evaluator<T>
| ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93:
required from âEigen::SparseMatrix<_Scalar, _Options, _StorageIndex>&
Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const
Eigen::SparseMatrixBase<OtherDerived>&) [with OtherDerived =
Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> >; _Scalar = double; int
_Options = 0; _StorageIndex = int]â
1181 | const bool needToTranspose = (Flags & RowMajorBit) !=
(internal::evaluator<OtherDerived>::Flags & RowMajorBit);
|
^~~~~
data_manipulation.cpp:27:23: required from here
27 | mat = mat.transpose();
| ^
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In
instantiation of âclass Eigen::DenseCoeffsBase<Eigen::SparseMatrix<double, 1,
int>, 0>â:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80:
required from âstruct
Eigen::internal::evaluator<Eigen::SparseCompressedBase<Eigen::SparseMatrix<double,
1, int> > >â
336 | typedef typename
DenseCoeffsBase<Derived,ReadOnlyAccessors>::CoeffReturnType CoeffReturnType;
|
^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8:
required from âstruct
Eigen::internal::evaluator<Eigen::SparseMatrix<double, 1, int> >â
1505 | struct evaluator<SparseMatrix<_Scalar,_Options,_StorageIndex> >
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93:
required from âEigen::SparseMatrix<_Scalar, _Options, _StorageIndex>&
Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const
Eigen::SparseMatrixBase<OtherDerived>&) [with OtherDerived =
Eigen::SparseMatrix<double, 1, int>; _Scalar = double; int _Options = 0;
_StorageIndex = int]â
1181 | const bool needToTranspose = (Flags & RowMajorBit) !=
(internal::evaluator<OtherDerived>::Flags & RowMajorBit);
|
^~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7:
required from âvoid Eigen::internal::set_from_triplets(const
InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with
InputIterator = __gnu_cxx::__normal_iterator<Eigen::Triplet<double>*,
std::vector<Eigen::Triplet<double> > >; SparseMatrixType =
Eigen::SparseMatrix<double, 0, int>; DupFunctor = scalar_sum_op<double,
double>]â
1063 | mat = trMat;
| ~~~~^~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92:
required from âvoid Eigen::SparseMatrix<_Scalar, _Flags,
_StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&)
[with InputIterators = __gnu_cxx::__normal_iterator<Eigen::Triplet<double>*,
std::vector<Eigen::Triplet<double> > >; _Scalar = double; int _Options = 0;
_StorageIndex = int]â
1110 | internal::set_from_triplets<InputIterators,
SparseMatrix<Scalar,_Options,_StorageIndex> >(begin, end, *this,
internal::scalar_sum_op<Scalar,Scalar>());
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
data_manipulation.cpp:111:31: required from here
111 | combined_mat.setFromTriplets(tripletList.begin(), tripletList.end());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30:
warning: ignoring attributes on template argument
âEigen::internal::packet_traits<double>::typeâ {aka â__m128dâ}
[-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
gcc -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/Rcpp/include'
-I'/usr/lib/R/site-library/RcppEigen/include' -fpic -g -O2
-ffile-prefix-map=/build/reproducible-path/r-base-4.5.2=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
valid_pointer.c -o valid_pointer.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o SeuratObject.so
RcppExports.o data_manipulation.o valid_pointer.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to
/<<PKGBUILDDIR>>/debian/r-cran-seuratobject/usr/lib/R/site-library/00LOCK-r-cran-seuratobject-5.3.0/00new/SeuratObject/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SeuratObject)
rm -f
/<<PKGBUILDDIR>>/debian/r-cran-seuratobject/usr/lib/R/site-library/SeuratObject/LICENSE
W: Ignoring specified R dependency: R (>= 4.1.0)
I: Using r-cran-sp for Depends:sp (>= 1.5.0)
I: Using r-bioc-delayedarray for Recommends:delayedarray
I: Using r-cran-fs for Recommends:fs (>= 1.5.2)
I: Version replacement between package version 1.0-0 and Debian version
1.0-24+dfsg-1
suspicious. Do not replace anything.
I: Using r-cran-sf by changing version to (>= 1.0-0) for Recommends:sf (>=
1.0-0)
I: Using r-cran-ggplot2 for Recommends:ggplot2
I: Using r-bioc-hdf5array for Recommends:hdf5array
I: Using r-cran-rmarkdown for Recommends:rmarkdown
I: Using r-cran-testthat for Recommends:testthat
W: Cannot find a debian package for Suggests:BPCells
I: Using r-cran-fs for Suggests:fs (>= 1.5.2)
I: Using r-cran-sf by changing version to (>= 1.0-0) for Suggests:sf (>= 1.0.0)
I: Using r-cran-future for Imports:future
I: Using r-cran-future.apply for Imports:future.apply
I: Using r-cran-generics for Imports:generics
I: Using r-cran-lifecycle for Imports:lifecycle
I: Version replacement between package version 1.6.4 and Debian version
1.7-4-1+b1
suspicious. Do not replace anything.
I: Using r-cran-matrix by changing version to (>= 1.6.4) for Imports:Matrix
(>= 1.6.4)
I: Using r-cran-progressr for Imports:progressr
I: Using r-cran-rcpp for Imports:Rcpp (>= 1.0.5)
I: Using r-cran-rlang for Imports:rlang (>= 0.4.7)
I: Using r-cran-spam for Imports:spam
I: Using r-cran-rcpp for LinkingTo:Rcpp
I: Using r-cran-rcppeigen for LinkingTo:RcppEigen
I: Use r-cran-seuratobject as Debian binary package for variables substitution
dh_installdocs -O--buildsystem=R
dh_installchangelogs -O--buildsystem=R
dh_installsystemduser -O--buildsystem=R
dh_perl -O--buildsystem=R
dh_link -O--buildsystem=R
dh_strip_nondeterminism -O--buildsystem=R
dh_compress -O--buildsystem=R
dh_fixperms -O--buildsystem=R
dh_missing -O--buildsystem=R
dh_dwz -a -O--buildsystem=R
dh_strip -a -O--buildsystem=R
dh_makeshlibs -a -O--buildsystem=R
dh_shlibdeps -a -O--buildsystem=R
dh_installdeb -O--buildsystem=R
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rmbversion=`dpkg -l r-cran-matrix | grep 'ii' | sed
's/^.*r-cran-matrix[[:space:]]\+\([0-9.-]\+\)[[:space:]]\+.*/\1/'`; \
sed -i "s/r-cran-matrix[^,]*/r-cran-matrix (>= ${rmbversion})/"
debian/*substvars
rversion=`dpkg -l r-base-core | grep 'ii' | sed
's/^.*r-base-core[[:space:]]\+\([0-9.-]\+\)-[0-9+b]\+[[:space:]]\+.*/\1/'`; \
sed -i "s/\(r-api-[0-9.]\+\),/& r-base-core (>= ${rversion})/" debian/*substvars
dh_gencontrol
dpkg-gencontrol: warning: cannot parse dependency r-cran-matrix (>= ii
r-cran-matrix 1.7-4-1+b1 amd64 GNU R package of classes for dense and
sparse matrices)
dpkg-gencontrol: error: parsing package 'r-cran-seuratobject' Depends field:
r-api-4.0, r-base-core (>= 4.5.2) , , r-cran-sp (>= 1.5.0), r-cran-future,
r-cran-future.apply, r-cran-generics, r-cran-lifecycle, r-cran-matrix (>= ii
r-cran-matrix 1.7-4-1+b1 amd64 GNU R package of classes for dense and
sparse matrices), r-cran-progressr, r-cran-rcpp (>= 1.0.5), r-cran-rlang (>=
0.4.7), r-cran-spam, r-cran-rcpp, r-cran-rcppeigen,
libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 14),
dh_gencontrol: error: dh_gencontrol: error: dpkg-gencontrol
-pr-cran-seuratobject -ldebian/changelog -Tdebian/r-cran-seuratobject.substvars
-cdebian/control -Pdebian/.debhelper/r-cran-seuratobject/dbgsym-root
-UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential
-UConflicts -DPriority=optional -UHomepage -UImportant
-DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using
-UStatic-Built-Using -DPackage=r-cran-seuratobject-dbgsym
-DDepends="r-cran-seuratobject (= \${binary:Version})" -DDescription="debug
symbols for r-cran-seuratobject"
-DBuild-Ids=d3af7cff912f865f69dc99c8a2bb86d3f517c80b -DSection=debug
-UMulti-Arch -UReplaces -UBreaks returned exit code 25
dh_gencontrol: error: Aborting due to earlier error
make[1]: *** [debian/rules:9: override_dh_gencontrol] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
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--- End Message ---
pgpE9nZvujt8f.pgp
