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This works fine when I am executing the steps on R command prompt. But when its done inside a function of a package, step 2 throws the following error :

Error in which(matA != 0, arr.ind = TRUE) :
  argument to 'which' is not logical
Here's the sample code with an example:
matA <- as(Matrix(c(0,1,2,1,0,0,3,0,2), nrow=3, ncol=3), "sparseMatrix")  # Step 1
nz <- which(matA != 0, arr.ind = TRUE)  # Step 2
     row col
[1,]   2   1
[2,]   3   1
[3,]   1   2
[4,]   1   3
[5,]   3   3
The loaded matrices in my case are of type: dsCMatrix, dgCMatrix.
class(matA != 0): lsCMatrix
I don't understand why should this lead to the error.
Please note the following:
Can't share the dumped sparse matrix file. Hence shown an example by creating a dummy matrix for step 1.
The dimensions of the sparse matrix are huge. So converting the sparse matrix to a regular matrix exceeds the memory limit.
Libraries:
The package that I am using mentions the following libraries:
Suggests: 
    testthat (>= 2.1.0),
    knitr,
    rmarkdown
Imports: 
    irlba,
    text2vec,
    dplyr,
    magrittr,
    Matrix,
    readr,
    rlang,
    data.table,
    stringr,
You need to load the library Matrix, chances are the package does not load it. See example below:
library(Seurat)
mat = pbmc_small@assays$RNA@counts
class(mat)
[1] "dgCMatrix"
attr(,"package")
[1] "Matrix"
which(mat>0)
Error in which(mat > 0) : argument to 'which' is not logical
library(Matrix)
head(which(mat>0,arr.ind=TRUE))
         row col
CD79B      2   1
HLA-DQB1   6   1
LTB        9   1
SP100     12   1
CXCR4     23   1
CD3D      31   1
If Matrix is already loaded, it might be the Matrix::which is masked somehow. you can do:
Matrix::which(mat>0)
                Inside the function, I have added print(dim(matA)).    And the script prints the following statement just before executing the above line: Loading required package: Matrix   So I guess the issue is not what you had mentioned.
– Kaushik Acharya
                Mar 2, 2020 at 10:40
                Ok hey, I tested it, there's no reason for it not to work. Can you try calling the which explicitly, using Matrix::which(matA > 0)
– StupidWolf
                Mar 2, 2020 at 11:01
                You are right. Explicitly calling Matrix::which worked. Seems the script was using which of another library.   Thanks a lot.
– Kaushik Acharya
                Mar 2, 2020 at 11:28
        
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