[R-sig-ME] glmmTMB installation

[Bingsong Zhang]

*Hi all,*

*Can anyone help to check what might be the problem of installation? I
tried to install from CRAN and github, but both failed. Below is the
message I got:*

/usr/local/apps/R/4.0/site-library_4.0.0/RcppEigen/include/Eigen/src/Core/Assign.h:66:28:
  required from ‘Derived& Eigen::MatrixBase<Derived>::operator=(const
Eigen::DenseBase<OtherDerived>&) [with OtherDerived =
Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0,
Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0,
Eigen::Stride<0, 0> >, 0>; Derived = Eigen::Map<Eigen::Matrix<double, -1,
-1>, 0, Eigen::Stride<0, 0> >]’
/spin1/home/linux/fanr/R/4.0/library/TMB/include/atomic_math.hpp:426:1:
required from ‘void atomic::matmul(const CppAD::vector<Type>&,
CppAD::vector<Type>&) [with Double = double]’
/spin1/home/linux/fanr/R/4.0/library/TMB/include/atomic_math.hpp:426:1:
required from ‘bool atomic::atomicmatmul<Type>::forward(size_t, size_t,
const CppAD::vector<bool>&, CppAD::vector<bool>&, const
CppAD::vector<Type>&, CppAD::vector<Type>&) [with Type = double; size_t =
long unsigned int]’
/spin1/home/linux/fanr/R/4.0/library/TMB/include/atomic_math.hpp:426:1:
required from here
/usr/local/apps/R/4.0/site-library_4.0.0/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8:
warning: ignoring attributes on template argument
‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’}
[-Wignored-attributes]
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [glmmTMB.o] Error 1
ERROR: compilation failed for package ‘glmmTMB’
* removing ‘/spin1/home/linux/fanr/R/4.0/library/glmmTMB’

The downloaded source packages are in
        ‘/tmp/RtmpofDpAq/downloaded_packages’
Warning message:
In install.packages("glmmTMB") :
  installation of package ‘glmmTMB’ had non-zero exit status

*There are many more actually, but these were the last part of the error
message.*

*Many thanks,*
*Bingsong*

On Wed, Oct 14, 2020 at 10:16 PM Bingsong Zhang <bz117 using georgetown.edu>
wrote:

> *Hi all,*
>
> *Can anyone help to check what might be the problem of installation? I
> tried to install from CRAN and github, but both failed. Below is the
> message I got:*
>
> /usr/local/apps/R/4.0/site-library_4.0.0/RcppEigen/include/Eigen/src/Core/Assign.h:66:28:
>   required from ‘Derived& Eigen::MatrixBase<Derived>::operator=(const
> Eigen::DenseBase<OtherDerived>&) [with OtherDerived =
> Eigen::Product<Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0,
> Eigen::Stride<0, 0> >, Eigen::Map<const Eigen::Matrix<double, -1, -1>, 0,
> Eigen::Stride<0, 0> >, 0>; Derived = Eigen::Map<Eigen::Matrix<double, -1,
> -1>, 0, Eigen::Stride<0, 0> >]’
> /spin1/home/linux/fanr/R/4.0/library/TMB/include/atomic_math.hpp:426:1:
> required from ‘void atomic::matmul(const CppAD::vector<Type>&,
> CppAD::vector<Type>&) [with Double = double]’
> /spin1/home/linux/fanr/R/4.0/library/TMB/include/atomic_math.hpp:426:1:
> required from ‘bool atomic::atomicmatmul<Type>::forward(size_t, size_t,
> const CppAD::vector<bool>&, CppAD::vector<bool>&, const
> CppAD::vector<Type>&, CppAD::vector<Type>&) [with Type = double; size_t =
> long unsigned int]’
> /spin1/home/linux/fanr/R/4.0/library/TMB/include/atomic_math.hpp:426:1:
> required from here
> /usr/local/apps/R/4.0/site-library_4.0.0/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:960:8:
> warning: ignoring attributes on template argument
> ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’}
> [-Wignored-attributes]
> g++: fatal error: Killed signal terminated program cc1plus
> compilation terminated.
> make: *** [glmmTMB.o] Error 1
> ERROR: compilation failed for package ‘glmmTMB’
> * removing ‘/spin1/home/linux/fanr/R/4.0/library/glmmTMB’
>
> The downloaded source packages are in
>         ‘/tmp/RtmpofDpAq/downloaded_packages’
> Warning message:
> In install.packages("glmmTMB") :
>   installation of package ‘glmmTMB’ had non-zero exit status
>
> *There are many more actually, but these were the last part of the error
> message.*
>
> *Many thanks,*
> *Bingsong*
>

	[[alternative HTML version deleted]]