search

Bioconductor / MatrixGenerics

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
https://bioconductor.org/packages/MatrixGenerics
12 stars 1 forks source link

Add default methods with user-friendly fallback mechanism #16

Closed hpages closed 3 years ago

hpages commented 3 years ago

This extends the fallback mechanism proposed here to all the generic functions defined in MatrixGenerics.

hpages commented 3 years ago

If nobody objects, I'll merge early next week. Thanks!

const-ae commented 3 years ago

Skimming over the code it looks good (I'll try to take a deeper look over the weekend, but can't promise anything). Don't forget to add yourself to the authors list :)

hpages commented 3 years ago

ok, let's proceed

PeteHaitch commented 3 years ago

Hmm, it's not quite working yet. Compare these 3 examples; depending on which sparseMatrixStats function is called first it either works or errors and subsequent functions may also be affected.

colMads() errors but colMedians() works

suppressPackageStartupMessages(library(MatrixGenerics))
library(Matrix)

set.seed(666)
x <- matrix(rpois(100, 3), ncol = 4)
X <- as(x, "dgCMatrix")

colMads(x) # Works
#> [1] 1.4826 1.4826 2.9652 1.4826
colMads(X) # Errors
#> Error in MatrixGenerics:::.load_next_suggested_package_to_search(x): Failed to find a colMads() method for dgCMatrix objects.

# Other functions work
colMedians(X) 
#> [1] 3 3 3 3
colMaxs(X) 
#> [1] 7 8 6 7

# But first function still fails
colMads(X)
#> Error in MatrixGenerics:::.load_next_suggested_package_to_search(x): Failed to find a colMads() method for dgCMatrix objects.

Created on 2020-10-13 by the reprex package (v0.3.0)

Session info ``` r devtools::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.0.2 (2020-06-22) #> os macOS Catalina 10.15.7 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Melbourne #> date 2020-10-13 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.10 2020-09-15 [1] #> BiocGenerics 0.35.4 2020-06-04 [1] #> callr 3.5.0 2020-10-08 [1] #> cli 2.1.0 2020-10-12 [1] #> crayon 1.3.4 2017-09-16 [1] #> DelayedArray 0.15.16 2020-10-06 [1] #> DelayedMatrixStats 1.11.1 2020-06-28 [1] #> desc 1.2.0 2018-05-01 [1] #> devtools 2.3.2 2020-09-18 [1] #> digest 0.6.25 2020-02-23 [1] #> ellipsis 0.3.1 2020-05-15 [1] #> evaluate 0.14 2019-05-28 [1] #> fansi 0.4.1 2020-01-08 [1] #> fs 1.5.0 2020-07-31 [1] #> glue 1.4.2 2020-08-27 [1] #> highr 0.8 2019-03-20 [1] #> htmltools 0.5.0 2020-06-16 [1] #> IRanges 2.23.10 2020-06-13 [1] #> knitr 1.30 2020-09-22 [1] #> lattice 0.20-41 2020-04-02 [1] #> magrittr 1.5 2014-11-22 [1] #> Matrix * 1.2-18 2019-11-27 [1] #> MatrixGenerics * 1.1.5 2020-10-12 [1] #> matrixStats * 0.57.0 2020-09-25 [1] #> memoise 1.1.0 2017-04-21 [1] #> pkgbuild 1.1.0 2020-07-13 [1] #> pkgload 1.1.0 2020-05-29 [1] #> prettyunits 1.1.1 2020-01-24 [1] #> processx 3.4.4 2020-09-03 [1] #> ps 1.4.0 2020-10-07 [1] #> R6 2.4.1 2019-11-12 [1] #> Rcpp 1.0.5 2020-07-06 [1] #> remotes 2.2.0 2020-07-21 [1] #> rlang 0.4.8 2020-10-08 [1] #> rmarkdown 2.4 2020-09-30 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> S4Vectors 0.27.14 2020-10-09 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> sparseMatrixStats 1.1.10 2020-10-06 [1] #> stringi 1.5.3 2020-09-09 [1] #> stringr 1.4.0 2019-02-10 [1] #> testthat 2.3.2 2020-03-02 [1] #> usethis 1.6.3 2020-09-17 [1] #> withr 2.3.0 2020-09-22 [1] #> xfun 0.18 2020-09-29 [1] #> yaml 2.2.1 2020-02-01 [1] #> source #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Bioconductor #> Bioconductor #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Github (Bioconductor/MatrixGenerics@18ebcb5) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ```

colMedians() errors but colMads() works

suppressPackageStartupMessages(library(MatrixGenerics))
library(Matrix)

set.seed(666)
x <- matrix(rpois(100, 3), ncol = 4)
X <- as(x, "dgCMatrix")

colMedians(x) # Works
#> [1] 3 3 3 3
colMedians(X) # Errors
#> Error in MatrixGenerics:::.load_next_suggested_package_to_search(x): Failed to find a colMedians() method for dgCMatrix objects.

# Other functions work
colMads(X) 
#> [1] 1.4826 1.4826 2.9652 1.4826
colMaxs(X) 
#> [1] 7 8 6 7

# But first function still fails
colMedians(X)
#> Error in MatrixGenerics:::.load_next_suggested_package_to_search(x): Failed to find a colMedians() method for dgCMatrix objects.

Created on 2020-10-13 by the reprex package (v0.3.0)

Session info ``` r devtools::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.0.2 (2020-06-22) #> os macOS Catalina 10.15.7 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Melbourne #> date 2020-10-13 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.10 2020-09-15 [1] #> BiocGenerics 0.35.4 2020-06-04 [1] #> callr 3.5.0 2020-10-08 [1] #> cli 2.1.0 2020-10-12 [1] #> crayon 1.3.4 2017-09-16 [1] #> DelayedArray 0.15.16 2020-10-06 [1] #> DelayedMatrixStats 1.11.1 2020-06-28 [1] #> desc 1.2.0 2018-05-01 [1] #> devtools 2.3.2 2020-09-18 [1] #> digest 0.6.25 2020-02-23 [1] #> ellipsis 0.3.1 2020-05-15 [1] #> evaluate 0.14 2019-05-28 [1] #> fansi 0.4.1 2020-01-08 [1] #> fs 1.5.0 2020-07-31 [1] #> glue 1.4.2 2020-08-27 [1] #> highr 0.8 2019-03-20 [1] #> htmltools 0.5.0 2020-06-16 [1] #> IRanges 2.23.10 2020-06-13 [1] #> knitr 1.30 2020-09-22 [1] #> lattice 0.20-41 2020-04-02 [1] #> magrittr 1.5 2014-11-22 [1] #> Matrix * 1.2-18 2019-11-27 [1] #> MatrixGenerics * 1.1.5 2020-10-12 [1] #> matrixStats * 0.57.0 2020-09-25 [1] #> memoise 1.1.0 2017-04-21 [1] #> pkgbuild 1.1.0 2020-07-13 [1] #> pkgload 1.1.0 2020-05-29 [1] #> prettyunits 1.1.1 2020-01-24 [1] #> processx 3.4.4 2020-09-03 [1] #> ps 1.4.0 2020-10-07 [1] #> R6 2.4.1 2019-11-12 [1] #> Rcpp 1.0.5 2020-07-06 [1] #> remotes 2.2.0 2020-07-21 [1] #> rlang 0.4.8 2020-10-08 [1] #> rmarkdown 2.4 2020-09-30 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> S4Vectors 0.27.14 2020-10-09 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> sparseMatrixStats 1.1.10 2020-10-06 [1] #> stringi 1.5.3 2020-09-09 [1] #> stringr 1.4.0 2019-02-10 [1] #> testthat 2.3.2 2020-03-02 [1] #> usethis 1.6.3 2020-09-17 [1] #> withr 2.3.0 2020-09-22 [1] #> xfun 0.18 2020-09-29 [1] #> yaml 2.2.1 2020-02-01 [1] #> source #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Bioconductor #> Bioconductor #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Github (Bioconductor/MatrixGenerics@18ebcb5) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ```

colMedians() and colMads() both work (everything works?)

suppressPackageStartupMessages(library(MatrixGenerics))
library(Matrix)

set.seed(666)
x <- matrix(rpois(100, 3), ncol = 4)
X <- as(x, "dgCMatrix")

colMaxs(x) # Works
#> [1] 7 8 6 7
colMaxs(X) # Works
#> [1] 7 8 6 7

# Other functions work
colMads(X) 
#> [1] 1.4826 1.4826 2.9652 1.4826
colMedians(X) 
#> [1] 3 3 3 3

Created on 2020-10-13 by the reprex package (v0.3.0)

Session info ``` r devtools::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.0.2 (2020-06-22) #> os macOS Catalina 10.15.7 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Melbourne #> date 2020-10-13 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.10 2020-09-15 [1] #> BiocGenerics 0.35.4 2020-06-04 [1] #> callr 3.5.0 2020-10-08 [1] #> cli 2.1.0 2020-10-12 [1] #> crayon 1.3.4 2017-09-16 [1] #> DelayedArray 0.15.16 2020-10-06 [1] #> DelayedMatrixStats 1.11.1 2020-06-28 [1] #> desc 1.2.0 2018-05-01 [1] #> devtools 2.3.2 2020-09-18 [1] #> digest 0.6.25 2020-02-23 [1] #> ellipsis 0.3.1 2020-05-15 [1] #> evaluate 0.14 2019-05-28 [1] #> fansi 0.4.1 2020-01-08 [1] #> fs 1.5.0 2020-07-31 [1] #> glue 1.4.2 2020-08-27 [1] #> highr 0.8 2019-03-20 [1] #> htmltools 0.5.0 2020-06-16 [1] #> IRanges 2.23.10 2020-06-13 [1] #> knitr 1.30 2020-09-22 [1] #> lattice 0.20-41 2020-04-02 [1] #> magrittr 1.5 2014-11-22 [1] #> Matrix * 1.2-18 2019-11-27 [1] #> MatrixGenerics * 1.1.5 2020-10-12 [1] #> matrixStats * 0.57.0 2020-09-25 [1] #> memoise 1.1.0 2017-04-21 [1] #> pkgbuild 1.1.0 2020-07-13 [1] #> pkgload 1.1.0 2020-05-29 [1] #> prettyunits 1.1.1 2020-01-24 [1] #> processx 3.4.4 2020-09-03 [1] #> ps 1.4.0 2020-10-07 [1] #> R6 2.4.1 2019-11-12 [1] #> Rcpp 1.0.5 2020-07-06 [1] #> remotes 2.2.0 2020-07-21 [1] #> rlang 0.4.8 2020-10-08 [1] #> rmarkdown 2.4 2020-09-30 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> S4Vectors 0.27.14 2020-10-09 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> sparseMatrixStats 1.1.10 2020-10-06 [1] #> stringi 1.5.3 2020-09-09 [1] #> stringr 1.4.0 2019-02-10 [1] #> testthat 2.3.2 2020-03-02 [1] #> usethis 1.6.3 2020-09-17 [1] #> withr 2.3.0 2020-09-22 [1] #> xfun 0.18 2020-09-29 [1] #> yaml 2.2.1 2020-02-01 [1] #> source #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Bioconductor #> Bioconductor #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> Github (Bioconductor/MatrixGenerics@18ebcb5) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.0) #> Bioconductor #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> CRAN (R 4.0.0) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.2) #> CRAN (R 4.0.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library ```
hpages commented 3 years ago

Oh no!

Method dispatch uses a cache mechanism to speedup method lookup. The 1st time colMads() was called the dispatch mechanism didn't find a method for dgCMatrix objects (sparseMatrixStats was not loaded yet) so it used the ANY method instead, and the association between dgCMatrix objects and the ANY method got stored in the cache. So from now on, no matter what, calling colMads() on a dgCMatrix will always go for the ANY method, even if sparseMatrixStats got loaded and there is now a dgCMatrix method in the method table.

Step by step:

suppressPackageStartupMessages(library(MatrixGenerics))
library(Matrix)

set.seed(666)
x <- matrix(rpois(100, 3), ncol = 4)
X <- as(x, "dgCMatrix")

This selects the ANY method, as expected:

selectMethod("colMads", "dgCMatrix")
# Method Definition:
# 
# function (x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, 
#     na.rm = FALSE, ...) 
# {
#     MatrixGenerics:::.load_next_suggested_package_to_search(x)
#     callGeneric()
# }
# <bytecode: 0x469af48>
# 
# Signatures:
#         x          
# target  "dgCMatrix"
# defined "ANY"      

showMethods("colMads")
# Function: colMads (package MatrixGenerics)
# x="ANY"
# x="matrix_OR_array_OR_table_OR_numeric"

After calling colMads(X), selectMethod() finds the dgCMatrix method:

colMads(X) # Errors

selectMethod("colMads", "dgCMatrix")
# Method Definition:
# 
# function (x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826, 
#     na.rm = FALSE, ...) 
# {
#     .local <- function (x, rows = NULL, cols = NULL, constant = 1.4826, 
#         na.rm = FALSE) 
#     {
#         if (!is.null(rows)) {
#             x <- x[rows, , drop = FALSE]
#         }
#         if (!is.null(cols)) {
#             x <- x[, cols, drop = FALSE]
#         }
#         dgCMatrix_colMads(x, na_rm = na.rm, scale_factor = constant)
#     }
#     .local(x, rows, cols, constant, na.rm, ...)
# }
# <bytecode: 0x8896e30>
# <environment: namespace:sparseMatrixStats>
# 
# Signatures:
#         x          
# target  "dgCMatrix"
# defined "dgCMatrix"

But showMethods() fails to see it (like method dispatch):

showMethods("colMads")
# Function: colMads (package MatrixGenerics)
# x="ANY"
# x="dgCMatrix"
#     (inherited from: x="ANY")
# x="matrix_OR_array_OR_table_OR_numeric"

Pretty nasty!

What's even more crazy is that trying to debug actually fixes the problem:

debug(colMads, signature="dgCMatrix")
# Tracing specified method for function "colMads" in environment
# <namespace:MatrixGenerics>

colMads(X)
# Tracing function ".local" in package "sparseMatrixStats"
# Tracing .local(x, rows, cols, constant, na.rm, ...) step 2 
# Called from: eval(expr, p)
# Browse[1]> 
# debug: if (!is.null(rows)) {
#     x <- x[rows, , drop = FALSE]
# }
# Browse[2]> 
# debug: if (!is.null(cols)) {
#     x <- x[, cols, drop = FALSE]
# }
# Browse[2]> 
# debug: dgCMatrix_colMads(x, na_rm = na.rm, scale_factor = constant)
# Browse[2]> 
# [1] 1.4826 1.4826 2.9652 1.4826

undebug(colMads, signature="dgCMatrix")
# Untracing specified method for function "colMads" in environment
# <namespace:MatrixGenerics>

Now showMethods() sees the dgCMatrix method:

showMethods("colMads")
Function: colMads (package MatrixGenerics)
x="ANY"
x="dgCMatrix"
x="matrix_OR_array_OR_table_OR_numeric"

## And from now on, colMads(X) works:
colMads(X)
# [1] 1.4826 1.4826 2.9652 1.4826

So calling colMads(X) inside a debug session somehow seems to flush the cache.

I'll try to come up with a fix. It's probably not gonna be pretty!

Thanks Pete!

hpages commented 3 years ago

Done: 7f900765e56d43e7257cf943ca2d21f66f3eb654 It's not too ugly.

I'll try to report the method dispatch bug later this week.

I'm not too keen on your suggestion to include the list of packages to install in the call to BiocManager::install() displayed in the error message Pete because in most cases people will probably not need to install all the suggested packages, only a few selected ones. For example they wouldn't need to install DelayedMatrixStats if they've never heard of DelayedArray objects and are only dealing with dgCMatrix objects.

H.

PeteHaitch commented 3 years ago

Gees, I'm glad I didn't have to deal with that, it's nasty.

I'm not too keen on your suggestion to include the list of packages to install in the call to BiocManager::install() displayed in the error message Pete because in most cases people will probably not need to install all the suggested packages, only a few selected ones. For example they wouldn't need to install DelayedMatrixStats if they've never heard of DelayedArray objects and are only dealing with dgCMatrix objects.

Ah I see. My read of the code was that it would only report the exactly relevant package but I see you're saying it may report a 'false positive' as well as the relevant package?

PeteHaitch commented 3 years ago

BTW any idea why colMaxs() worked immediately?

hpages commented 3 years ago

BTW any idea why colMaxs() worked immediately?

Great observation. That's going to be useful when I try to come up with a useful bug report.

I'm not sure why. The only difference with colMads() is where the methods are defined:

When colMads() or colMaxs() is called, MatrixGenerics:::.load_next_suggested_package_to_search() tries to load the suggested packages in order until dispatch finds an appropriate method. If the supplied object is a dgCMatrix, loading sparseMatrixStats should be enough. However, before the 7f900765e56d43e7257cf943ca2d21f66f3eb654 fix, calling colMads() or colMaxs() was triggering the loading of both packages, sparseMatrixStats and DelayedMatrixStats, because the method dispatch bug would prevent dispatch from finding the method after sparseMatrixStats gets loaded. The difference I see between colMads() and colMaxs() though is that for the latter, the loading of DelayedMatrixStats puts the dgCMatrix method back in the output of showMethods("dgCMatrix"). It does this with colMaxs() but not with colMads(). Probably related to the fact that the DelayedMatrixStats package defines a method for the latter but not for the former. Even though I don't have a clear picture of what's going on exactly.

Anyway, this is an heisenbug, the first one I ever have to deal with in R. They are the worst!

On the BiocManager::install() command that gets displayed when a method is not found:

After giving it a 2nd thought, when the list of packages to install is reduced to one package, it makes sense to insert the name of the package in the call to BiocManager::install() displayed in the error message. There is no ambiguity about what package to install in that case. So with e988bc31cc114171376396878fa214555f60ad7b we get:

> colMads(X)
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : 
  Failed to find a colMads() method for dgCMatrix objects.
  However, the following packages are likely to contain the missing method
  but are not installed: sparseMatrixStats, DelayedMatrixStats.
  Please install them (with 'BiocManager::install(...)') and try again.
  Alternatively, if you know where the missing method is defined, install
  only that package.

if sparseMatrixStats and DelayedMatrixStats are not installed, and:

> colMads(X)
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : 
  Failed to find a colMads() method for dgCMatrix objects.
  However, the following package is likely to contain the missing method
  but is not installed: sparseMatrixStats.
  Please install it (with 'BiocManager::install("sparseMatrixStats")')
  and try again.

if only sparseMatrixStats is not installed.

hpages commented 3 years ago

huh, looks like MatrixGenerics is getting a little download boost... and that's only the beginning