search for: csparse_validate

...hat): library(Matrix); sparseMatrix(1,1) # 1 x 1 sparse Matrix of class "ngCMatrix" # # [1,] | suppressPackageStartupMessages(library(SeuratObject)) sparseMatrix(1,1) # 1 x 1 sparse Matrix of class "ngCMatrix" # Error in validityMethod(as(object, superClass)) : # object 'Csparse_validate' not found detach('package:SeuratObject', unload = TRUE); sparseMatrix(1,1) # 1 x 1 sparse Matrix of class "ngCMatrix" # Error in validityMethod(as(object, superClass)) : # object 'Csparse_validate' not found detach('package:Matrix', unload = TRUE); library(M...

...nstalling the older Matrix, next installs SeuratObject, and then by removing the older Matrix making the (already installed) current Matrix version the default. This simulates a package update for Matrix. Which, as the final snippet demonstrates, silently breaks SeuratObject as the cached S4 method Csparse_validate is now missing. So when SeuratObject was installed under Matrix 1.5.1, it becomes unuseable under Matrix 1.6.0. What this shows is that a call to update.packages() will silently corrupt an existing installation. We understand that this was known and addressed at CRAN by rebuilding all binary pack...

...1) > # 1 x 1 sparse Matrix of class "ngCMatrix" > # > # [1,] | > suppressPackageStartupMessages(library(SeuratObject)) > sparseMatrix(1,1) > # 1 x 1 sparse Matrix of class "ngCMatrix" > # Error in validityMethod(as(object, superClass)) : > # object 'Csparse_validate' not found > detach('package:SeuratObject', unload = TRUE); sparseMatrix(1,1) > # 1 x 1 sparse Matrix of class "ngCMatrix" > # Error in validityMethod(as(object, superClass)) : > # object 'Csparse_validate' not found > detach('package:Matrix',...