*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*
glmmTMB installation
4 messages · Bingsong Zhang, Andrew Johnson, Ben Bolker
*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 at 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*
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 at curtin.edu.au Web | www.curtin.edu.au CRICOS Provider Code 00301J -----Original Message----- From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> On Behalf Of Bingsong Zhang Sent: Friday, 16 October 2020 9:08 AM To: R-sig-mixed-models at 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 at 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*
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
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 at curtin.edu.au Web | www.curtin.edu.au CRICOS Provider Code 00301J -----Original Message----- From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> On Behalf Of Bingsong Zhang Sent: Friday, 16 October 2020 9:08 AM To: R-sig-mixed-models at 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 at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models