Error when install packages that loading dbplyr as the dependency

[albert-ying]

I encountered a weird bug while installing packages with dbplyr as a dependency

Example 1: Tune package

install.packages("tune")

trying URL 'https://cran.microsoft.com/src/contrib/tune_0.1.3.tar.gz'
Content type 'application/octet-stream' length 1056081 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘tune’ ...
** package ‘tune’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Loading required package: 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’
Warning: namespace ‘recipes’ is not available and has been replaced
by .GlobalEnv when processing object ‘ames_wflow’
Loading required package: 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’
Warning: namespace ‘recipes’ is not available and has been replaced
by .GlobalEnv when processing object ‘ames_wflow’
** inst
** byte-compile and prepare package for lazy loading
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’
Error in .requirePackage(package) :
  unable to find required package ‘dbplyr’
Calls: <Anonymous> ... .recacheSubclasses -> getClassDef -> .requirePackage
Execution halted
ERROR: lazy loading failed for package ‘tune’
* removing ‘/home/kying/R/x86_64-pc-linux-gnu-library/4.0/tune’

The downloaded source packages are in
	‘/tmp/RtmpO11XE2/downloaded_packages’
Warning message:
In install.packages("tune") :
  installation of package ‘tune’ had non-zero exit status

Example 2: glmnet package

install.packages("glmnet")

Installing package into ‘/home/kying/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.microsoft.com/src/contrib/glmnet_4.1-1.tar.gz'
Content type 'application/octet-stream' length 2154483 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package ‘glmnet’ ...
** package ‘glmnet’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran  -fpic  -g -O2  -c glmnet5dpclean.f -o glmnet5dpclean.o
gcc -std=gnu99 -I"/home/kying/R/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c glmnet_init.c -o glmnet_init.o
gcc -std=gnu99 -I"/home/kying/R/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c pb.c -o pb.o
gfortran  -fpic  -g -O2  -c wls.f -o wls.o
gcc -std=gnu99 -shared -L/home/kying/R/lib/R/lib -L/usr/local/lib -o glmnet.so glmnet5dpclean.o glmnet_init.o pb.o wls.o -L/usr/lib/gcc/x86_64-linux-gnu/5 -lgfortran -lm -lquadmath -L/home/kying/R/lib/R/lib -lR
installing to /home/kying/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-glmnet/00new/glmnet/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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’
Error: package or namespace load failed for ‘Matrix’ in .requirePackage(package):
 unable to find required package ‘dbplyr’
Error: package ‘Matrix’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘glmnet’
* removing ‘/home/kying/R/x86_64-pc-linux-gnu-library/4.0/glmnet’
* restoring previous ‘/home/kying/R/x86_64-pc-linux-gnu-library/4.0/glmnet’

The downloaded source packages are in
	‘/tmp/RtmpO11XE2/downloaded_packages’
Warning message:
In install.packages("glmnet") :
  installation of package ‘glmnet’ had non-zero exit status

dbplyr itself can be installed with no error

> install.packages("dbplyr")
Installing package into ‘/home/kying/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cran.microsoft.com/src/contrib/dbplyr_2.1.0.tar.gz'
Content type 'application/octet-stream' length 579687 bytes (566 KB)
==================================================
downloaded 566 KB

* installing *source* package ‘dbplyr’ ...
** package ‘dbplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dbplyr)

The downloaded source packages are in
	‘/tmp/RtmpO11XE2/downloaded_packages’

Do you have any thoughts that what may cause this error? Thank you!

SessionInfo

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /home/kying/R/lib/R/lib/libRblas.so
LAPACK: /home/kying/R/lib/R/lib/libRlapack.so

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

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

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3

[albert-ying]

Resolved by manually install the package "Matrix"

[anikaliu]

I'm having the same issue as mentioned above and wasn't able to solve this by installing and loading dbplyr and Matrix in advance. Do you have any suggestions on how to work around this?

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’
Error in .requirePackage(package) : 
  unable to find required package ‘dbplyr’
Calls: <Anonymous> ... .recacheSubclasses -> getClassDef -> .requirePackage
Execution halted

[jamesdalg]

I will affirm that this issue still occurs when using version 2.1.1.

> library(GenomicFeatures)
Loading required package: AnnotationDbi
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 ‘GenomicFeatures’:
 .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’
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                           LC_TIME=English_United States.1252    
system code page: 65001

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] InteractionSet_1.20.0       SummarizedExperiment_1.22.0 Biobase_2.52.0              MatrixGenerics_1.4.3        matrixStats_0.61.0          foreach_1.5.2               parallelsugar_0.0.0.2      
 [8] gUtils_0.2.0                data.table_1.14.2           GenomicRanges_1.44.0        GenomeInfoDb_1.28.4         IRanges_2.26.0              S4Vectors_0.30.2            BiocGenerics_0.38.0        
[15] magrittr_2.0.2             

loaded via a namespace (and not attached):
  [1] utf8_1.2.2               proto_1.0.0              tidyselect_1.1.1         lme4_1.1-28              RSQLite_2.2.9            AnnotationDbi_1.54.1     htmlwidgets_1.5.4        grid_4.1.2              
  [9] BiocParallel_1.26.2      ggtern_3.3.5             munsell_0.5.0            codetools_0.2-18         DT_0.20                  miniUI_0.1.1.1           Brobdingnag_1.2-7        colorspace_2.0-2        
 [17] knitr_1.37               rstudioapi_0.13          robustbase_0.93-9        bayesm_3.1-4             brms_2.16.3              bayesplot_1.8.1          rstan_2.21.3             repr_1.1.4              
 [25] GenomeInfoDbData_1.2.6   bit64_4.0.5              farver_2.1.0             bridgesampling_1.1-2     coda_0.19-4              vctrs_0.3.8              generics_0.1.2           xfun_0.29               
 [33] R6_2.5.1                 markdown_1.1             doParallel_1.0.17        gamm4_0.2-6              projpred_2.0.2           bitops_1.0-7             cachem_1.0.6             DelayedArray_0.18.0     
 [41] assertthat_0.2.1         promises_1.2.0.1         BiocIO_1.2.0             scales_1.1.1             gtable_0.3.0             processx_3.5.2           rlang_1.0.1              splines_4.1.2           
 [49] rtracklayer_1.52.1       checkmate_2.0.0          inline_0.3.19            yaml_2.2.2               reshape2_1.4.4           abind_1.4-5              threejs_0.3.3            crosstalk_1.2.0         
 [57] backports_1.4.1          httpuv_1.6.5             rsconnect_0.8.25         tensorA_0.36.2           tools_4.1.2              ggplot2_3.3.5            ellipsis_0.3.2           posterior_1.2.0         
 [65] ggridges_0.5.3           latex2exp_0.9.3          Rcpp_1.0.8               plyr_1.8.6               base64enc_0.1-3          progress_1.2.2           zlibbioc_1.38.0          purrr_0.3.4             
 [73] RCurl_1.98-1.6           ps_1.6.0                 prettyunits_1.1.1        zoo_1.8-9                ggrepel_0.9.1            colourpicker_1.1.1       mvtnorm_1.1-3            hms_1.1.1               
 [81] shinyjs_2.1.0            mime_0.12                xtable_1.8-4             shinystan_2.5.0          XML_3.99-0.8             gridExtra_2.3            rstantools_2.1.1         compiler_4.1.2          
 [89] tibble_3.1.6             crayon_1.4.2             minqa_1.2.4              StanHeaders_2.21.0-7     htmltools_0.5.2          mgcv_1.8-38              later_1.3.0              tidyr_1.2.0             
 [97] RcppParallel_5.1.5       DBI_1.1.2                MASS_7.3-55              boot_1.3-28              compositions_2.0-4       Matrix_1.4-0             cli_3.1.1                igraph_1.2.11           
[105] forcats_0.5.1            pkgconfig_2.0.3          GenomicAlignments_1.28.0 skimr_2.1.3              dygraphs_1.1.1.6         XVector_0.32.0           stringr_1.4.0            distributional_0.3.0    
[113] callr_3.7.0              digest_0.6.29            Biostrings_2.60.2        restfulr_0.0.13          shiny_1.7.1              Rsamtools_2.8.0          gtools_3.9.2             rjson_0.2.21            
[121] nloptr_2.0.0             lifecycle_1.0.1          nlme_3.1-155             jsonlite_1.7.3           BSgenome_1.60.0          fansi_1.0.2              pillar_1.7.0             lattice_0.20-45         
[129] loo_2.4.1                KEGGREST_1.32.0          fastmap_1.1.0            httr_1.4.2               DEoptimR_1.0-10          pkgbuild_1.3.1           glue_1.6.1               xts_0.12.1              
[137] png_0.1-7                shinythemes_1.2.0        iterators_1.0.14         bit_4.0.4                stringi_1.7.6            blob_1.2.2               memoise_2.0.1            dplyr_1.0.8             
>