Error in rowVars(p) : could not find function "rowVars"

[alexw-gsct]

I am getting the following error:

dmlt = DSS::DMLtest(bs, group1, group2, equal.disp = FALSE, smoothing = FALSE, BPPARAM = BiocParallel::SnowParam(2))
Estimating dispersion for each CpG site, this will take a while ...
Error in rowVars(p) : could not find function "rowVars"

This error means I cannot use DMLtest without loading library(DSS) (which itself loads many other downstream packages). Perhaps specify the namespace e.g. calling MatrixGenerics::rowVars(p) ?

[haowulab]

rowVars is a function from matrixStats package, which should be automatically loaded into R. Maybe your R version is old. Please update to the latest one.

[alexw-gsct]

I am running R 4.0.3 and using Bioconductor devel 3.12.

I also use matrixStats for its row statistics functions and can confirm it does not automatically load.

See below reprex:
path = file.path(system.file(package="DSS"), "extdata")

dat1.1 = read.table(file.path(path, "cond1_1.txt"), header=TRUE)
dat1.2 = read.table(file.path(path, "cond1_2.txt"), header=TRUE)
dat2.1 = read.table(file.path(path, "cond2_1.txt"), header=TRUE)
dat2.2 = read.table(file.path(path, "cond2_2.txt"), header=TRUE)
BSobj = DSS::makeBSseqData( list(dat1.1, dat1.2, dat2.1, dat2.2),

•                    c("C1","C2", "N1", "N2") )[1:1000,]
  

dmlTest = DSS::DMLtest(BSobj, group1=c("C1", "C2"), group2=c("N1", "N2"))
Estimating dispersion for each CpG site, this will take a while ...
Error in rowVars(p) : could not find function "rowVars"
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252

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

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 compiler_4.0.3 GenomeInfoDb_1.25.11 XVector_0.29.3
[5] R.methodsS3_1.8.1 R.utils_2.10.1 MatrixGenerics_1.1.8 bitops_1.0-6
[9] rhdf5filters_1.1.3 DSS_2.37.0 tools_4.0.3 DelayedMatrixStats_1.11.5
[13] zlibbioc_1.35.0 BSgenome_1.57.7 lifecycle_0.2.0 rhdf5_2.33.11
[17] lattice_0.20-41 rlang_0.4.8 Matrix_1.2-18 rstudioapi_0.11
[21] DelayedArray_0.15.16 parallel_4.0.3 GenomeInfoDbData_1.2.4 bsseq_1.25.7
[25] rtracklayer_1.49.5 Biostrings_2.57.2 S4Vectors_0.27.14 gtools_3.8.2
[29] IRanges_2.23.10 stats4_4.0.3 locfit_1.5-9.4 grid_4.0.3
[33] Biobase_2.49.1 data.table_1.13.2 R6_2.4.1 HDF5Array_1.17.14
[37] XML_3.99-0.5 BiocParallel_1.23.3 limma_3.45.19 Rhdf5lib_1.11.3
[41] GenomicAlignments_1.25.3 Rsamtools_2.5.3 scales_1.1.1 matrixStats_0.57.0
[45] sparseMatrixStats_1.1.11 splines_4.0.3 BiocGenerics_0.35.4 GenomicRanges_1.41.6
[49] SummarizedExperiment_1.19.9 permute_0.9-5 colorspace_1.4-1 RCurl_1.98-1.2
[53] munsell_0.5.0 crayon_1.3.4 R.oo_1.24.0

The function works after DSS is loaded; presumably rowVars using namespace MatrixGenerics is used.

suppressPackageStartupMessages(library(DSS))
dmlTest = DSS::DMLtest(BSobj, group1=c("C1", "C2"), group2=c("N1", "N2"))
Estimating dispersion for each CpG site, this will take a while ...
|===============================================================================================================| 100%

|===============================================================================================================| 100%

[haowulab]

Yeah you are right. I have library(matrixStats) in my .Rprofile. My bad. I'll update the package to use matrixStats::rowVars.

I never used MatrixGenerics, seems like a new package. And I don't even have it installed in my R. I guess some other packages load matrixStats.

BTW, is there particular reason why you don't want to load DSS?

[alexw-gsct]

Thanks Haowu.

I am developing a package and it's just my habit of loading as few packages as possible so I know their namespace dependencies when I finalise the functions.

Your package imports bsseq, which imports DelayedMatrixStats, which depends MatrixGenerics and imports matrixStats. bsseq also imports a whole bunch of other packages, which I try to avoid as it helps in debugging which package is breaking the code.

[haowulab]

I've modified the package and committed the changes. Do you want a copy of the package? It'll take some time until the changes appear on bioc. Or you can just modify that yourself.

[alexw-gsct]

Thanks. I have installed using devtools::install_github. Can now confirm the above example now works without loading library