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class definition removed from ‘dbplyr’ #1356

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ASKurz opened this issue May 15, 2022 · 14 comments
Closed

class definition removed from ‘dbplyr’ #1356

ASKurz opened this issue May 15, 2022 · 14 comments
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@ASKurz
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ASKurz commented May 15, 2022

Since installing brms 2.17.3, I've noticed a new quirk that if I load brms before the tidyverse, I get an error.

library(brms)
library(tidyverse)

Error in completeSubclasses(classDef2, class1, obj, where) : 
  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
Error: package or namespace load failed for ‘tidyverse’:
 .onLoad failed in loadNamespace() for 'dbplyr', details:
  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
  error: error in contained classes ("character") for class “ident”; class definition removed from ‘dbplyr’

However, there is no such error if I start a fresh R session and load the two in the reverse order.

library(tidyverse)
library(brms)

Here's my sessionInfo().

sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] brms_2.17.3     Rcpp_1.0.8.3    forcats_0.5.1   stringr_1.4.0   dplyr_1.0.9     purrr_0.3.4    
 [7] readr_2.1.2     tidyr_1.2.0     tibble_3.1.7    ggplot2_3.3.6   tidyverse_1.3.1

loaded via a namespace (and not attached):
  [1] TH.data_1.1-1        colorspace_2.0-3     ellipsis_0.3.2       ggridges_0.5.3      
  [5] estimability_1.3     markdown_1.1         base64enc_0.1-3      fs_1.5.2            
  [9] rstudioapi_0.13      farver_2.1.0         rstan_2.26.11        DT_0.22             
 [13] fansi_1.0.3          mvtnorm_1.1-3        lubridate_1.8.0      xml2_1.3.3          
 [17] splines_4.2.0        bridgesampling_1.1-2 codetools_0.2-18     shinythemes_1.2.0   
 [21] bayesplot_1.9.0      jsonlite_1.8.0       broom_0.8.0          dbplyr_2.1.1        
 [25] shiny_1.7.1          compiler_4.2.0       httr_1.4.3           emmeans_1.7.3       
 [29] backports_1.4.1      assertthat_0.2.1     Matrix_1.4-1         fastmap_1.1.0       
 [33] cli_3.3.0            later_1.3.0          htmltools_0.5.2      prettyunits_1.1.1   
 [37] tools_4.2.0          igraph_1.3.1         coda_0.19-4          gtable_0.3.0        
 [41] glue_1.6.2           reshape2_1.4.4       posterior_1.2.1      V8_4.1.0            
 [45] cellranger_1.1.0     vctrs_0.4.1          nlme_3.1-157         crosstalk_1.2.0     
 [49] tensorA_0.36.2       ps_1.7.0             rvest_1.0.2          mime_0.12           
 [53] miniUI_0.1.1.1       lifecycle_1.0.1      gtools_3.9.2         MASS_7.3-56         
 [57] zoo_1.8-10           scales_1.2.0         colourpicker_1.1.1   hms_1.1.1           
 [61] promises_1.2.0.1     Brobdingnag_1.2-7    sandwich_3.0-1       parallel_4.2.0      
 [65] inline_0.3.19        shinystan_2.6.0      curl_4.3.2           gridExtra_2.3       
 [69] loo_2.5.1            StanHeaders_2.26.11  stringi_1.7.6        dygraphs_1.1.1.6    
 [73] checkmate_2.1.0      pkgbuild_1.3.1       rlang_1.0.2          pkgconfig_2.0.3     
 [77] matrixStats_0.62.0   distributional_0.3.0 lattice_0.20-45      rstantools_2.2.0    
 [81] htmlwidgets_1.5.4    tidyselect_1.1.2     processx_3.5.3       plyr_1.8.7          
 [85] magrittr_2.0.3       R6_2.5.1             generics_0.1.2       multcomp_1.4-19     
 [89] DBI_1.1.2            pillar_1.7.0         haven_2.5.0          withr_2.5.0         
 [93] xts_0.12.1           survival_3.3-1       abind_1.4-5          modelr_0.1.8        
 [97] crayon_1.5.1         utf8_1.2.2           tzdb_0.3.0           grid_4.2.0          
[101] readxl_1.4.0         callr_3.7.0          threejs_0.3.3        reprex_2.0.1        
[105] digest_0.6.29        xtable_1.8-4         httpuv_1.6.5         RcppParallel_5.1.5  
[109] stats4_4.2.0         munsell_0.5.0        shinyjs_2.1.0
@paul-buerkner
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I think I have seen this error before (someone had posted it somewhere) but I don't really know what to you about it. Also, while it is triggered by loading brms, I do not see how it relates to anything specifically brms does. Does anyone have any idea whats going on?

@munoztd0
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Same issue here, trying to found out. If anyone has any info I would be very interested.

@paul-buerkner
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paul-buerkner commented May 17, 2022 via email

@eipi10
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eipi10 commented May 18, 2022

I was having the same problem. Based on this dbplyr issue I reinstalled the Matrix package and that eliminated the error (though I have no idea what's causing the error or why reinstalling Matrix resolves it).

@ASKurz
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ASKurz commented May 18, 2022

Reinstalling Matrix didn't work, on my end.

@munoztd0
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Me neither

@eipi10
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eipi10 commented May 18, 2022

A few minutes ago I upgraded from brms 2.17.0 to 2.17.3 and the error came back. I reinstalled Matrix but it also did not work for me this time.

@JBris
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JBris commented May 28, 2022 •
edited
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I just ran into the same issue. Reinstalling Matrix fixed it for me.

I'm using brms 2.17.0 too

@ASKurz
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ASKurz commented May 28, 2022

For me, the issue didn't arise until I installed brms 2.17.3.

mdahirel added a commit to mdahirel/Tetranychus-metapop-2019 that referenced this issue Jun 13, 2022
@mdahirel
invert loading order of brms and tidyverse to prevent bug
03cac6b 
bug (tidyverse doesn't load and gives error) doesn't appear on all machines, and may disappear and reappear with brms or tidyverse updates

loading tidyverse before brms consistently prevents it

documented here: paul-buerkner/brms#1356
@munoztd0
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munoztd0 commented Jul 8, 2022 •
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Issue has been fixed, for more info check out tidyverse/dbplyr/issues/779 (well actually it is Brobdingnag which caused the bug which is a dependency from bridgsampling).

Just need to install dev version of Brobdingnag (>= 1.2-8) and reload.

devtools::install_github("RobinHankin/Brobdingnag")

@paul-buerkner
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Perfect! Thank you!

@dputhier
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dputhier commented Feb 24, 2023 •
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Hi. I got the same issue:

	> library(dbplyr)
	Error in completeSubclasses(classDef2, class1, obj, where) : 
	  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
	Error: package or namespace load failed for ‘dbplyr’:
	 .onLoad failed in loadNamespace() for 'dbplyr', details:
	  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
	  error: error in contained classes ("character") for class “ident”; class definition removed from ‘dbplyr’

I have installed the latest Brobdingnag version:

            devtools::install_github("RobinHankin/Brobdingnag")

Restarted R:

          .rs.restartR()

Reinstalled dbplyr:

         install.packages('dbplyr')

But still got the issue:

	> library('dbplyr')
	Error in completeSubclasses(classDef2, class1, obj, where) : 
	  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
	Error: package or namespace load failed for ‘dbplyr’:
	 .onLoad failed in loadNamespace() for 'dbplyr', details:
	  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
	  error: error in contained classes ("character") for class “ident”; class definition removed from ‘dbplyr’

I also tried to install from github

             devtools::install_github("tidyverse/dbplyr")

But unfortunately got another error message

	> library('dbplyr')
	Error: package or namespace load failed for ‘dbplyr’ in get(Info[i, 1], envir = env):
	 lazy-load database '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/dbplyr/R/dbplyr.rdb' is corrupt
	In addition: Warning message:
	In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1

I deleted the '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/dbplyr'

            rm -rf /Library/Frameworks/R.framework/Versions/4.2/Resources/library/dbplyr

Re-installed the github version:

             .rs.restartR()
             devtools::install_github("tidyverse/dbplyr")

Whithout more success:

	> library('dbplyr')
	Error in completeSubclasses(classDef2, class1, obj, where) : 
	  trying to get slot "subclasses" from an object of a basic class ("NULL") with no slots
	Error: package or namespace load failed for ‘dbplyr’:
	 .onLoad failed in loadNamespace() for 'dbplyr', details:
	  call: setClass(cl, contains = c(prevClass, "VIRTUAL"), where = where)
	  error: error in contained classes ("character") for class “ident”; class definition removed from ‘dbplyr’

Any hint ?
Best

	> sessionInfo()
	R version 4.2.2 (2022-10-31)
	Platform: x86_64-apple-darwin17.0 (64-bit)
	Running under: macOS Monterey 12.5.1

	Matrix products: default
	LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

	locale:
	[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

	other attached packages:
	[1] Brobdingnag_1.2-9 Matrix_1.5-1     

	loaded via a namespace (and not attached):
	  [1] Seurat_4.3.0           Rtsne_0.16             colorspace_2.1-0       deldir_1.0-6           gson_0.0.9            
	  [6] ellipsis_0.3.2         ggridges_0.5.4         rprojroot_2.0.3        fs_1.6.1               rstudioapi_0.14       
	 [11] spatstat.data_3.0-0    leiden_0.4.3           listenv_0.9.0          remotes_2.4.2          ggrepel_0.9.3         
	 [16] fansi_1.0.4            codetools_0.2-18       splines_4.2.2          cachem_1.0.6           pkgload_1.3.2         
	 [21] polyclip_1.10-4        jsonlite_1.8.4         ica_1.0-3              cluster_2.1.4          png_0.1-8             
	 [26] uwot_0.1.14            shiny_1.7.4            sctransform_0.3.5      spatstat.sparse_3.0-0  compiler_4.2.2        
	 [31] httr_1.4.4             SeuratObject_4.1.3     fastmap_1.1.0          lazyeval_0.2.2         cli_3.6.0             
	 [36] later_1.3.0            prettyunits_1.1.1      htmltools_0.5.4        tools_4.2.2            igraph_1.4.0          
	 [41] gtable_0.3.1           glue_1.6.2             RANN_2.6.1             reshape2_1.4.4         dplyr_1.1.0           
	 [46] Rcpp_1.0.10            scattermore_0.8        Biobase_2.58.0         vctrs_0.5.2            spatstat.explore_3.0-6
	 [51] nlme_3.1-160           progressr_0.13.0       lmtest_0.9-40          spatstat.random_3.1-3  stringr_1.5.0         
	 [56] ps_1.7.2               globals_0.16.2         mime_0.12              miniUI_0.1.1.1         lifecycle_1.0.3       
	 [61] irlba_2.3.5.1          devtools_2.4.5         goftest_1.2-3          future_1.31.0          MASS_7.3-58.1         
	 [66] zoo_1.8-11             scales_1.2.1           promises_1.2.0.1       spatstat.utils_3.0-1   parallel_4.2.2        
	 [71] SparseM_1.81           RColorBrewer_1.1-3     curl_5.0.0             memoise_2.0.1          reticulate_1.28       
	 [76] pbapply_1.7-0          gridExtra_2.3          ggplot2_3.4.1          stringi_1.7.12         desc_1.4.2            
	 [81] S4Vectors_0.36.1       BiocGenerics_0.44.0    pkgbuild_1.4.0         rlang_1.0.6            pkgconfig_2.0.3       
	 [86] matrixStats_0.63.0     bitops_1.0-7           lattice_0.20-45        ROCR_1.0-11            purrr_1.0.1           
	 [91] tensor_1.5             patchwork_1.1.2        htmlwidgets_1.6.1      processx_3.8.0         cowplot_1.1.1         
	 [96] tidyselect_1.2.0       parallelly_1.34.0      RcppAnnoy_0.0.20       plyr_1.8.8             magrittr_2.0.3        
	[101] R6_2.5.1               profvis_0.3.7          generics_0.1.3         DBI_1.1.3              withr_2.5.0           
	[106] pillar_1.8.1           fitdistrplus_1.1-8     survival_3.4-0         abind_1.4-5            RCurl_1.98-1.10       
	[111] sp_1.6-0               tibble_3.1.8           future.apply_1.10.0    crayon_1.5.2           KernSmooth_2.23-20    
	[116] utf8_1.2.3             spatstat.geom_3.0-6    plotly_4.10.1          urlchecker_1.0.1       usethis_2.1.6         
	[121] grid_4.2.2             data.table_1.14.6      callr_3.7.3            digest_0.6.31          xtable_1.8-4          
	[126] tidyr_1.3.0            httpuv_1.6.8           stats4_4.2.2           munsell_0.5.0          viridisLite_0.4.1     
	[131] sessioninfo_1.2.2

@jingydz
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jingydz commented Mar 1, 2023

image
image
I have tried to install Brobdingnag (>= 1.2-8) , Matrix, rbms and etc. But that still doesn't solve my problem.

@cparsania
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cparsania commented Mar 4, 2024 •
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With Brobdingnag_1.2-9 still the same issue.

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8 participants
@eipi10 @dputhier @cparsania @paul-buerkner @JBris @ASKurz @munoztd0 @jingydz