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edzer / sdsr

Spatial Data Science: With Applications in R (source files)
https://r-spatial.org/book
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new error in Ch 16 #116

Closed edzer closed 11 months ago

edzer commented 11 months ago

We see a new error in this action

Quitting from lines 180-184 [unnamed-chunk-12] (16-SpatialRegression.qmd)
1080 Error in `initializePtr()`:
1081 ! function 'cholmod_factor_ldetA' not provided by package 'Matrix'
1082 Backtrace:
1083   1. lme4::lmer(...)
1084   3. lme4 (local) `<fn>`(...)
1085   5. methods (local) `<rfMthdDf>`(...)
1086   6. methods::new(def, ...)
1087   8. methods::initialize(value, ...)
1088   9. .Object$initialize(...)
1089  10. lme4 (local) initializePtr()

@rsbivand is this something you could look at?

rsbivand commented 11 months ago

Completion without errors with:

> source("16-SpatialRegression.R", echo=TRUE)
...
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora Linux 39 (Workstation Edition)

Matrix products: default
BLAS:   /home/rsb/topics/R/R432-share/lib64/R/lib/libRblas.so 
LAPACK: /home/rsb/topics/R/R432-share/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Oslo
tzcode source: system (glibc)

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] INLA_23.04.24    foreach_1.5.2    R2BayesX_1.1-5   mgcv_1.9-0      
 [5] nlme_3.1-163     colorspace_2.1-0 BayesXsrc_3.0-4  spatialreg_1.2-9
 [9] hglm_2.2-1       hglm.data_1.0-1  sp_2.1-1         MASS_7.3-60     
[13] lme4_1.1-35.1    Matrix_1.6-1.1   spData_2.3.0     sf_1.0-14       

loaded via a namespace (and not attached):
 [1] s2_1.1.4           sandwich_3.0-2     utf8_1.2.4         generics_0.1.3    
 [5] class_7.3-22       spDataLarge_2.0.6  LearnBayes_2.15.1  KernSmooth_2.23-22
 [9] lattice_0.22-5     magrittr_2.0.3     grid_4.3.2         iterators_1.0.14  
[13] mvtnorm_1.2-3      e1071_1.7-13       DBI_1.1.3          survival_3.5-7    
[17] multcomp_1.4-25    fansi_1.0.5        TH.data_1.1-2      codetools_0.2-19  
[21] cli_3.6.1          rlang_1.1.2        expm_0.999-7       units_0.8-4       
[25] splines_4.3.2      tools_4.3.2        deldir_1.0-9       nloptr_2.0.3      
[29] coda_0.19-4        minqa_1.2.6        dplyr_1.1.3        boot_1.3-28.1     
[33] vctrs_0.6.4        R6_2.5.1           matrixStats_1.1.0  zoo_1.8-12        
[37] proxy_0.4-27       lifecycle_1.0.4    classInt_0.4-10    spdep_1.2-8       
[41] pkgconfig_2.0.3    pillar_1.9.0       glue_1.6.2         Rcpp_1.0.11       
[45] xfun_0.41          tibble_3.2.1       tidyselect_1.2.0   knitr_1.45        
[49] wk_0.9.0           compiler_4.3.2

Note Matrix_1.6-1.1 and lme4_1.1-35.1 https://cran.r-project.org/web/packages/lme4/news.html; I also see Matrix_1.6-2 on CRAN from yesterday, try again - no error:

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora Linux 39 (Workstation Edition)

Matrix products: default
BLAS:   /home/rsb/topics/R/R432-share/lib64/R/lib/libRblas.so 
LAPACK: /home/rsb/topics/R/R432-share/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Oslo
tzcode source: system (glibc)

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] INLA_23.04.24    foreach_1.5.2    R2BayesX_1.1-5   mgcv_1.9-0      
 [5] nlme_3.1-163     colorspace_2.1-0 BayesXsrc_3.0-4  spatialreg_1.2-9
 [9] hglm_2.2-1       hglm.data_1.0-1  sp_2.1-1         MASS_7.3-60     
[13] lme4_1.1-35.1    Matrix_1.6-2     spData_2.3.0     sf_1.0-14       

loaded via a namespace (and not attached):
 [1] s2_1.1.4           sandwich_3.0-2     utf8_1.2.4         generics_0.1.3    
 [5] class_7.3-22       spDataLarge_2.0.6  LearnBayes_2.15.1  KernSmooth_2.23-22
 [9] lattice_0.22-5     magrittr_2.0.3     grid_4.3.2         iterators_1.0.14  
[13] mvtnorm_1.2-3      e1071_1.7-13       DBI_1.1.3          survival_3.5-7    
[17] multcomp_1.4-25    fansi_1.0.5        TH.data_1.1-2      codetools_0.2-19  
[21] cli_3.6.1          rlang_1.1.2        expm_0.999-7       units_0.8-4       
[25] splines_4.3.2      tools_4.3.2        deldir_1.0-9       nloptr_2.0.3      
[29] coda_0.19-4        minqa_1.2.6        dplyr_1.1.3        boot_1.3-28.1     
[33] vctrs_0.6.4        R6_2.5.1           matrixStats_1.1.0  zoo_1.8-12        
[37] proxy_0.4-27       lifecycle_1.0.4    classInt_0.4-10    spdep_1.2-8       
[41] pkgconfig_2.0.3    pillar_1.9.0       glue_1.6.2         Rcpp_1.0.11       
[45] xfun_0.41          tibble_3.2.1       tidyselect_1.2.0   knitr_1.45        
[49] wk_0.9.0           compiler_4.3.2

On balance a version of lme4 that wasn't in synch with Matrix. Does GA actually snapshop sessionInfo?

edzer commented 11 months ago

Thanks! Sounds indeed like a false positive; in that case it should be resolved in 1-2 days.

edzer commented 11 months ago

Seems like this summarizes it pretty well: https://stat.ethz.ch/pipermail/r-package-devel/2023q4/010051.html