3

I just try to use :

scRNA <- FindNeighbors(scRNA, dims = pc.num)

and

scRNA.counts <- Read10X(data.dir = "filtered_feature_bc_matrix")

and both of them gives error like :

Error in validityMethod(as(object, superClass)) :    object 'Matrix_validate' not found

I guess these code totally run well in other's computer

so I wonder what's wrong with my code and how to fix it ?

zx8754
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bohrxd
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    I suspect that you need to update Matrix to version 1.5-x: `update.packages("Matrix")`. Having said that, the fact that the symbol was not found suggests that at least one reverse dependency of Matrix is missing `>= 1.5-0` in its `DESCRIPTION` file. – Mikael Jagan Sep 13 '22 at 10:31
  • Please, bohrxd, do mention the R *package* name of the functions you use, which would help pin pointing the "culpable" package that needs to add `(>= 1.5-0)` after its `Matrix` dependency. – Martin Mächler Sep 13 '22 at 16:06
  • thanks for everyone , the good news is that it works after I re-installed the package'Matrix' to >= 1.5-0 – bohrxd Sep 14 '22 at 02:29

2 Answers2

1

Indeed, to solve the problem for you, it should be sufficient to do what @Mikael Jagan says:

update.packages("Matrix")

2nd thought: The above may not solve the problem entirely: As there are other packages involved, some of these may have to be re-installed (after the updating of Matrix).

Can you post the output (or good summary of that if it's too long) of

 traceback()

immediately after producing the error you are seeing?

Martin Mächler
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0

Try doing this before function calls:

Matrix_validate = "CsparseMatrix_validate"
user4020650
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    Your answer could be improved with additional supporting information. Please [edit] to add further details, such as citations or documentation, so that others can confirm that your answer is correct. You can find more information on how to write good answers [in the help center](/help/how-to-answer). – Community Aug 25 '23 at 17:40