[R-pkg-team] Bug#1127535: r-cran-seuratobject: FTBFS: 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,

Santiago Vila sanvila at debian.org
Mon Feb 9 18:05:44 GMT 2026 

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 ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
   56 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
   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 ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
  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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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 ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
  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 ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
  555 | class DenseCoeffsBase<Derived, DirectWriteAccessors>
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
   41 | template<typename Derived> class DenseBase
      |                                  ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
   48 | template<typename Derived> class MatrixBase
      |                                  ^~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
   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 ‘class Eigen::Matrix<double, 4, 1>’
  178 | class Matrix
      |       ^~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:   required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
   46 |   typedef typename Coefficients::CoeffReturnType CoeffReturnType;
      |                                                  ^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7:   required from ‘class Eigen::Quaternion<double>’
  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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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 ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:   required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >’
   36 | class SparseCompressedBase
      |       ^~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7:   required from ‘class Eigen::SparseMatrix<double, 0, int>’
   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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
   47 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> > >’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:   required from ‘class Eigen::SparseCompressedBase<Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> > >’
   36 | class SparseCompressedBase
      |       ^~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:22:9:   required from ‘class Eigen::internal::SparseTransposeImpl<Eigen::SparseMatrix<double, 0, int>, 1024>’
   22 |   class SparseTransposeImpl<MatrixType,CompressedAccessBit>
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:45:37:   required from ‘class Eigen::TransposeImpl<Eigen::SparseMatrix<double, 0, int>, Eigen::Sparse>’
   45 | template<typename MatrixType> class TransposeImpl<MatrixType,Sparse>
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37:   required from ‘class Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> >’
   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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
   47 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, -1>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, -1, -1> >’
   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 ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, -1> >’
   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 ‘class Eigen::Matrix<double, -1, -1>’
  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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes]
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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 ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 1>’
  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 ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, -1, -1>, 3>’
  555 | class DenseCoeffsBase<Derived, DirectWriteAccessors>
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, -1, -1> >’
   41 | template<typename Derived> class DenseBase
      |                                  ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, -1> >’
   48 | template<typename Derived> class MatrixBase
      |                                  ^~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, -1> >’
   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 ‘class Eigen::Matrix<double, -1, -1>’
  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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
   56 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 1, int> >’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:   required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 1, int> >’
   36 | class SparseCompressedBase
      |       ^~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7:   required from ‘class Eigen::SparseMatrix<double, 1, int>’
   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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
   47 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::SparseMatrix<double, 0, int>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> > >’
  336 |   typedef typename DenseCoeffsBase<Derived,ReadOnlyAccessors>::CoeffReturnType CoeffReturnType;
      |                                                                                ^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseMatrix<double, 0, int> >’
 1505 | struct evaluator<SparseMatrix<_Scalar,_Options,_StorageIndex> >
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseTranspose.h:58:63:   required from ‘struct Eigen::internal::unary_evaluator<Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> >, Eigen::internal::IteratorBased, double>’
   58 |     typedef typename evaluator<ArgType>::InnerIterator        EvalIterator;
      |                                                               ^~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:90:8:   required from ‘struct Eigen::internal::evaluator<Eigen::Transpose<Eigen::SparseMatrix<double, 0, int> > >’
   90 | struct evaluator : public unary_evaluator<T>
      |        ^~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93:   required from ‘Eigen::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]’
 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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
   56 |                      >::type PacketReturnType;
      |                              ^~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::SparseMatrix<double, 1, int>, 0>’:
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 1, int> > >’
  336 |   typedef typename DenseCoeffsBase<Derived,ReadOnlyAccessors>::CoeffReturnType CoeffReturnType;
      |                                                                                ^~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseMatrix<double, 1, int> >’
 1505 | struct evaluator<SparseMatrix<_Scalar,_Options,_StorageIndex> >
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93:   required from ‘Eigen::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]’
 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 ‘void 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>]’
 1063 |   mat = trMat;
      |   ~~~~^~~~~~~
/usr/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92:   required from ‘void 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]’
 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 ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-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
--------------------------------------------------------------------------------

More information about the R-pkg-team mailing list