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XiangyunHuang / data-analysis-in-action

:book: R 语言数据分析实战（写作中） Data Analysis in Action Using R
https://bookdown.org/xiangyun/data-analysis-in-action/
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Test with Fedora 39 and Quarto 1.4.489 #121

Closed XiangyunHuang closed 10 months ago

XiangyunHuang commented 10 months ago
XiangyunHuang commented 10 months ago 
Quitting from lines 615-619 [unnamed-chunk-44] (hierarchical-normal-models.qmd)
Error in `fitTMB()`:
! negative log-likelihood is NaN at starting parameter values
Backtrace:
 1. glmmTMB::glmmTMB(...)
 2. glmmTMB::fitTMB(TMBStruc)
Execution halted

Error: Process completed with exit code 1.

在 Matrix 更新后，TMB 和 glmmTMB 最好从源码重新安装或等二者更新后从 CRAN 安装。特别是 Matrix 包发布重大版本更新后，TMB 和 glmmTMB 必须更新，否则，结果会出问题。

XiangyunHuang commented 10 months ago 

Error in validObject(.Object) : 
  invalid class “dsparseModelMatrix” object: superclass "xMatrix" not defined in the environment of the object's class

 *** inla.core.safe:  inla.program has crashed: rerun to get better initial values. try=1/1 
Error in validObject(.Object) : 
  invalid class “dsparseModelMatrix” object: superclass "xMatrix" not defined in the environment of the object's class
Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts,  : 
  *** Failed to get good enough initial values. Maybe it is due to something else.

原因是 INLA 23.9.9 与新版 Matrix 1.6.2 不兼容（Matrix 1.6.2 发布很多更新），需要等待新版 Matrix 或 INLA 发布之后，再看。

XiangyunHuang commented 10 months ago

安装 Matrix 旧版本 1.6.-1.1 可以暂时解决此问题

XiangyunHuang commented 10 months ago

目前的开发版 Matrix 1.6-3 和 INLA 23.11.12 也不行，报错如下

Error in validObject(.Object) : 
  invalid class “dsparseModelMatrix” object: superclass "xMatrix" not defined in the environment of the object's class

只有回滚 Matrix 版本或重装 MatrixModels 才行，原因是 https://github.com/hrue/r-inla/issues/85

github-actions[bot] commented 10 months ago

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