[R-sig-ME] glmmTMB installation

[Andrew Johnson]

Hi Bingsong,

Can you open an issue over on the glmmTMB github: https://github.com/glmmTMB/glmmTMB/issues? It's a bit easier than troubleshooting over the list, and it's helpful to have the resolution available for others to find if they have a similar issue.

Cheers,
Andrew

Dr Andrew Johnson
BPsych(Hons), MBiostat, PhD, GStat.
Research Associate | School of Psychology

Curtin University 
Email | andrew.johnson using curtin.edu.au 
Web | www.curtin.edu.au 



CRICOS Provider Code 00301J 


-----Original Message-----
From: R-sig-mixed-models <r-sig-mixed-models-bounces using r-project.org> On Behalf Of Bingsong Zhang
Sent: Friday, 16 October 2020 9:08 AM
To: R-sig-mixed-models using r-project.org
Subject: Re: [R-sig-ME] glmmTMB installation

*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*
>

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