[R-sig-ME] glmmTMB installation

[Ben Bolker]

   I agree with Andrew.

   My best guess based on what I can see is that

* most of the warnings are irrelevant chaff (using 
CXXFLAGS+=-Wno-ignored-attributes in a .R/Makevars file helps enormously 
with this)
* the actual problem is running out of memory during compilation (in my 
experience this is the most common cause of out-of-the-blue 'killed' errors)

On 10/15/20 10:10 PM, Andrew Johnson wrote:
> 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*
>>
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>