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Commit final revdep results
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hadley committed Sep 6, 2024
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5 changes: 4 additions & 1 deletion revdep/README.md
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@@ -1,6 +1,6 @@
# Revdeps

## Failed to check (210)
## Failed to check (213)

|package |version |error |warning |note |
|:-----------------------|:----------|:-----|:-------|:----|
Expand Down Expand Up @@ -55,6 +55,7 @@
|DrugSim2DR |? | | | |
|DRviaSPCN |? | | | |
|ech |0.1.3 |1 | | |
|EcoEnsemble |1.1.0 |1 | | |
|ecolottery |1.0.0 |1 | | |
|EdSurvey |4.0.7 |1 | | |
|EpiEstim |2.2-4 |1 | | |
Expand All @@ -69,6 +70,7 @@
|GeneSelectR |? | | | |
|geomorph |? | | | |
|gJLS2 |0.2.0 |1 | | |
|gllvm |1.4.3 |1 | | |
|gmoTree |? | | | |
|gpuR |2.0.6 |1 | | |
|hettx |0.1.3 |1 | | |
Expand Down Expand Up @@ -108,6 +110,7 @@
|MRZero |0.2.0 |1 | | |
|MultiKink |0.2.0 |1 | | |
|multilevelTools |0.1.1 |1 | | |
|multinma |0.7.1 |1 | | |
|mvDFA |0.0.4 |1 | | |
|MXM |1.5.5 |1 | | |
|nebula |1.5.3 |1 | | |
Expand Down
7 changes: 5 additions & 2 deletions revdep/cran.md
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@@ -1,9 +1,9 @@
## revdepcheck results

We checked 8798 reverse dependencies (8788 from CRAN + 10 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
We checked 8826 reverse dependencies (8816 from CRAN + 10 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

* We saw 18 new problems
* We failed to check 200 packages
* We failed to check 203 packages

Issues with CRAN packages are summarised below.

Expand Down Expand Up @@ -117,6 +117,7 @@ Issues with CRAN packages are summarised below.
* DrugSim2DR (NA)
* DRviaSPCN (NA)
* ech (NA)
* EcoEnsemble (NA)
* ecolottery (NA)
* EdSurvey (NA)
* EpiEstim (NA)
Expand All @@ -129,6 +130,7 @@ Issues with CRAN packages are summarised below.
* GeneNMF (NA)
* GeneSelectR (NA)
* gJLS2 (NA)
* gllvm (NA)
* gpuR (NA)
* hettx (NA)
* Hmisc (NA)
Expand Down Expand Up @@ -166,6 +168,7 @@ Issues with CRAN packages are summarised below.
* MRZero (NA)
* MultiKink (NA)
* multilevelTools (NA)
* multinma (NA)
* mvDFA (NA)
* MXM (NA)
* nebula (NA)
Expand Down
234 changes: 234 additions & 0 deletions revdep/failures.md
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Expand Up @@ -3555,6 +3555,84 @@ ERROR: lazy loading failed for package ‘ech’
* removing ‘/tmp/workdir/ech/old/ech.Rcheck/ech’


```
# EcoEnsemble
<details>
* Version: 1.1.0
* GitHub: https://github.com/CefasRepRes/EcoEnsemble
* Source code: https://github.com/cran/EcoEnsemble
* Date/Publication: 2024-08-19 17:20:06 UTC
* Number of recursive dependencies: 91
Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info
</details>
## In both
* checking whether package ‘EcoEnsemble’ can be installed ... ERROR
```
Installation failed.
See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details.
```
## Installation
### Devel
```
* installing *source* package ‘EcoEnsemble’ ...
** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17


g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o
In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
...
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_withdrivers_namespace::model_ensemble_model_hierarchical_withdrivers; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
| ^~~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical_withdrivers.o] Error 1
ERROR: compilation failed for package ‘EcoEnsemble’
* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’


```
### CRAN
```
* installing *source* package ‘EcoEnsemble’ ...
** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17


g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o
In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
...
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_withdrivers_namespace::model_ensemble_model_hierarchical_withdrivers; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
| ^~~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical_withdrivers.o] Error 1
ERROR: compilation failed for package ‘EcoEnsemble’
* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’


```
# ecolottery
Expand Down Expand Up @@ -4471,6 +4549,84 @@ ERROR: lazy loading failed for package ‘gJLS2’
* removing ‘/tmp/workdir/gJLS2/old/gJLS2.Rcheck/gJLS2’


```
# gllvm
<details>
* Version: 1.4.3
* GitHub: https://github.com/JenniNiku/gllvm
* Source code: https://github.com/cran/gllvm
* Date/Publication: 2023-09-18 15:00:02 UTC
* Number of recursive dependencies: 67
Run `revdepcheck::cloud_details(, "gllvm")` for more info
</details>
## In both
* checking whether package ‘gllvm’ can be installed ... ERROR
```
Installation failed.
See ‘/tmp/workdir/gllvm/new/gllvm.Rcheck/00install.out’ for details.
```
## Installation
### Devel
```
* installing *source* package ‘gllvm’ ...
** package ‘gllvm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/opt/R/4.3.1/lib/R/site-library/TMB/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -c gllvm.cpp -o gllvm.o
In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /opt/R/4.3.1/lib/R/site-library/TMB/include/TMB.hpp:92,
from gllvm.cpp:2:
...
/opt/R/4.3.1/lib/R/site-library/TMB/include/tiny_ad/atomic.hpp:30:1: required from ‘void atomic::bessel_kOp<order, ninput, noutput, mask>::reverse(TMBad::ReverseArgs<Type>&) [with Type = double; int order = 3; int ninput = 2; int noutput = 8; long int mask = 9]
/opt/R/4.3.1/lib/R/site-library/TMB/include/TMBad/global.hpp:1721:28: required from ‘void TMBad::global::AddForwardMarkReverseMark<OperatorBase>::reverse(TMBad::ReverseArgs<Type>&) [with Type = double; OperatorBase = TMBad::global::AddIncrementDecrement<TMBad::global::AddDependencies<TMBad::global::AddInputSizeOutputSize<atomic::bessel_kOp<3, 2, 8, 9> > > >]
/opt/R/4.3.1/lib/R/site-library/TMB/include/TMBad/global.hpp:2134:57: required from ‘void TMBad::global::Complete<OperatorBase>::reverse(TMBad::ReverseArgs<double>&) [with OperatorBase = atomic::bessel_kOp<3, 2, 8, 9>]
/opt/R/4.3.1/lib/R/site-library/TMB/include/TMBad/global.hpp:2134:10: required from here
/opt/R/4.3.1/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]
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:200: gllvm.o] Error 1
ERROR: compilation failed for package ‘gllvm’
* removing ‘/tmp/workdir/gllvm/new/gllvm.Rcheck/gllvm’


```
### CRAN
```
* installing *source* package ‘gllvm’ ...
** package ‘gllvm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DTMBAD_FRAMEWORK -I'/opt/R/4.3.1/lib/R/site-library/TMB/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -c gllvm.cpp -o gllvm.o
In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /opt/R/4.3.1/lib/R/site-library/TMB/include/TMB.hpp:92,
from gllvm.cpp:2:
...
/opt/R/4.3.1/lib/R/site-library/TMB/include/tiny_ad/atomic.hpp:30:1: required from ‘void atomic::bessel_kOp<order, ninput, noutput, mask>::reverse(TMBad::ReverseArgs<Type>&) [with Type = double; int order = 3; int ninput = 2; int noutput = 8; long int mask = 9]
/opt/R/4.3.1/lib/R/site-library/TMB/include/TMBad/global.hpp:1721:28: required from ‘void TMBad::global::AddForwardMarkReverseMark<OperatorBase>::reverse(TMBad::ReverseArgs<Type>&) [with Type = double; OperatorBase = TMBad::global::AddIncrementDecrement<TMBad::global::AddDependencies<TMBad::global::AddInputSizeOutputSize<atomic::bessel_kOp<3, 2, 8, 9> > > >]
/opt/R/4.3.1/lib/R/site-library/TMB/include/TMBad/global.hpp:2134:57: required from ‘void TMBad::global::Complete<OperatorBase>::reverse(TMBad::ReverseArgs<double>&) [with OperatorBase = atomic::bessel_kOp<3, 2, 8, 9>]
/opt/R/4.3.1/lib/R/site-library/TMB/include/TMBad/global.hpp:2134:10: required from here
/opt/R/4.3.1/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]
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:200: gllvm.o] Error 1
ERROR: compilation failed for package ‘gllvm’
* removing ‘/tmp/workdir/gllvm/old/gllvm.Rcheck/gllvm’


```
# gmoTree
Expand Down Expand Up @@ -7179,6 +7335,84 @@ ERROR: lazy loading failed for package ‘multilevelTools’
* removing ‘/tmp/workdir/multilevelTools/old/multilevelTools.Rcheck/multilevelTools’


```
# multinma
<details>
* Version: 0.7.1
* GitHub: https://github.com/dmphillippo/multinma
* Source code: https://github.com/cran/multinma
* Date/Publication: 2024-06-11 12:20:06 UTC
* Number of recursive dependencies: 152
Run `revdepcheck::cloud_details(, "multinma")` for more info
</details>
## In both
* checking whether package ‘multinma’ can be installed ... ERROR
```
Installation failed.
See ‘/tmp/workdir/multinma/new/multinma.Rcheck/00install.out’ for details.
```
## Installation
### Devel
```
* installing *source* package ‘multinma’ ...
** package ‘multinma’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17


g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
...
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
| ^~~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1
ERROR: compilation failed for package ‘multinma’
* removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’


```
### CRAN
```
* installing *source* package ‘multinma’ ...
** package ‘multinma’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17


g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205,
...
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]
/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
| ^~~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1
ERROR: compilation failed for package ‘multinma’
* removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’


```
# mvDFA
Expand Down

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