Fail to install version 1.12.2

[derbalkon]

Hi, I'm getting some troubles installing version 1.12.2 recently. Every time I try to install the latest DelayedMatrixStats package, it always prompts up these error messages:

* installing *source* package ‘DelayedMatrixStats’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error : in method for ‘colAvgsPerRowSet’ with signature ‘X="DelayedMatrix"’:  arguments (‘na.rm’, ‘tFUN’) after ‘...’ in the generic must appear in the method, in the same place at the end of the argument list
Error: unable to load R code in package ‘DelayedMatrixStats’
Execution halted
ERROR: lazy loading failed for package ‘DelayedMatrixStats’
* removing ‘/usr/local/lib/R/4.0/site-library/DelayedMatrixStats’
* restoring previous ‘/usr/local/lib/R/4.0/site-library/DelayedMatrixStats’

Here's my session info:

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin20.2.0 (64-bit)
Running under: macOS  11.1

Matrix products: default
BLAS:   /usr/local/Cellar/openblas/0.3.13/lib/libopenblasp-r0.3.13.dylib
LAPACK: /usr/local/Cellar/r/4.0.3_2/lib/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.0.3

I have also tried to install it on a new virtual machine, still no luck. Then I checked the build report page, found the multiple platform builds are all failed with the same errors as mine. Perhaps something related to dependency has changed lately?

[renozao]

Also have this issue.
The method definition must be edited to match the generic in package MatrixGenerics:

setGeneric("colAvgsPerRowSet", function(X, W = NULL, cols = NULL, S, FUN = colMeans,  ..., na.rm = NA, tFUN = FALSE) standardGeneric("colAvgsPerRowSet"),
           signature = "X"
)

Currently the method is defined as follows, so one would need to add argument na.rm:

setMethod("colAvgsPerRowSet", "DelayedMatrix",
          function(X, W = NULL, cols = NULL, S, FUN = colMeans, ...,
                   force_block_processing = FALSE, tFUN = FALSE) {
# ...
}

[PeteHaitch]

I'm on leave but I'll take a look when back on Friday.

[PeteHaitch]

@hpages would you be able to fix this before then? I think it would need to be patched in release and devel

[bbimber]

We're hitting this as well

[XimenaBo]

Hi, has this been fixed, by any chance?
Thanks!

[bbimber]

If anyone wants a stopgap, I think this is a fix:

devtools::install_github("bbimber/DelayedMatrixStats", ref = "RELEASE_3_12")

Here's a PR #75. I dont know what it takes to push out a new version. @PeteHaitch @hpages - it seems like a lot of people would appreciate if there's a way to push a fixed version.

[rschauner]

If anyone wants a stopgap, I think this is a fix:

devtools::install_version("bbimber/DelayedMatrixStats", ref = "RELEASE_3_12")

Here's a PR #75. I dont know what it takes to push out a new version. @PeteHaitch @hpages - it seems like a lot of people would appreciate if there's a way to push a fixed version.

Thanks for your quick workaround. Trying to set up an HPC to run what I need to and this was the last thing I needed to install. However, I did need to change your code to this devtools::install_github("bbimber/DelayedMatrixStats", ref = "RELEASE_3_12") to get it to work.

[XimenaBo]

Thanks for your quick workaround. Trying to set up an HPC to run what I need to and this was the last thing I needed to install. However, I did need to change your code to this devtools::install_github("bbimber/DelayedMatrixStats", ref = "RELEASE_3_12") to get it to work.

Awesome, thank you both!

[bbimber]

yeah, should have been install_github. I've done little testing of my change, but it does at least build.

[hpages]

I pushed Aaron's fix today to the git repo hosted at git.bioconductor.org. Will take about 36 hours to propagate and become available via BiocManager::install(). If you can't wait, you can get this new version by cloning https://git.bioconductor.org/packages/DelayedMatrixStats.

Remember to switch to the RELEASE_3_12 branch (DelayedMatrixStats 1.12.3) if you're using BioC 3.12 (current release). The master branch (DelayedMatrixStats 1.13.5) is for BioC devel only.

@PeteHaitch Don't forget to resync the GitHub repo when you are back.

H.

[PeteHaitch]

Thanks, @LTLA for the PR and @hpages for pushing to git.bioconductor.org. I've been able to sync with GitHub as I'm back from camping a little earlier than originally planned.