DelayedArray loading Warning causes stop in Bioconductor 3.12
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inzirio ▴ 10
@inzirio-13571
Last seen 11 months ago

Hi,

I'm developing a package which has multiple dependencies (mainly SingleCellExperiment).

Since I started to use Bioconductor v3.12 on R v4.0.1 it started to not install my package from github anymore giving me this error:

Error: package or namespace load failed for ‘DelayedArray’:
 (converted from warning) multiple methods tables found for ‘which’
Error: package ‘DelayedArray’ could not be loaded
Execution halted

Then looking at the loading of the DelayedArray package I get this warning:

> library("DelayedArray")
Loading required package: stats4
Loading required package: matrixStats
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
    parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Warning message:
multiple methods tables found for ‘which’

Did anyone got the same issue?

Thanks, Dario

DelayedArray warning installation • 598 views
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@herve-pages-1542
Last seen 7 hours ago
Seattle, WA, United States

Hi Dario,

Please always provide your sessionInfo() as indicated in our Posting Guide.

Looks like you are using BioC devel (3.12) and that you have out-of-sync packages. BioC devel is changing fast so make sure to run BiocManager::install() often when you work with it. If the problem persists after that, run BiocManager::valid() and do whatever it tells you to do.

Hope this helps.

Best

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BiocManager::valid() returns TRUE for me, but I still see the warning. Here's my sessionInfo()

> BiocManager::valid()
[1] TRUE
> sessionInfo()
R version 4.0.0 Patched (2020-05-14 r78465)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ma38727/bin/R-4-0-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-4-0-branch/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] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] DelayedArray_0.15.1 IRanges_2.23.9      S4Vectors_0.27.12
[4] BiocGenerics_0.35.4 matrixStats_0.56.0

loaded via a namespace (and not attached):
[1] compiler_4.0.0  Matrix_1.2-18   grid_4.0.0      lattice_0.20-41

In a new R session, I can make it an error by saying options(warn = 2).

> options(warn=2)
> suppressPackageStartupMessages(library(DelayedArray))
Error: package or namespace load failed for 'DelayedArray':
 (converted from warning) multiple methods tables found for 'which'
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Entering edit mode

Hi Harvè,

thanks for replying (here and on slack), I write here for continuity.

I give you a reproducible example with the following code. This is the command used to install my package (Note that if I install it locally, it gives me no Error, but only Warnings)

install_github("drighelli/SpatialExperiment", ref="spatialExperiment")

Here it is my sessionInfo. I removed my entire library and installed everything from zero. (the SpatialExperiment package is loaded because I installed it in local with devtools::install())

> sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SpatialExperiment_0.0.99    SingleCellMultiModal_1.1.5  MultiAssayExperiment_1.15.2
 [4] SingleCellExperiment_1.11.4 SummarizedExperiment_1.19.5 Biobase_2.49.0             
 [7] GenomicRanges_1.41.5        GenomeInfoDb_1.25.1         DelayedArray_0.15.1        
[10] IRanges_2.23.9              S4Vectors_0.27.12           BiocGenerics_0.35.4        
[13] matrixStats_0.56.0          devtools_2.3.0              usethis_1.6.1              

loaded via a namespace (and not attached):
 [1] httr_1.4.1                    pkgload_1.1.0                
 [3] bit64_0.9-7                   AnnotationHub_2.20.0         
 [5] shiny_1.4.0.2                 assertthat_0.2.1             
 [7] interactiveDisplayBase_1.26.3 BiocManager_1.30.10          
 [9] BiocFileCache_1.12.0          blob_1.2.1                   
[11] GenomeInfoDbData_1.2.3        yaml_2.2.1                   
[13] remotes_2.1.1                 sessioninfo_1.1.1            
[15] BiocVersion_3.12.0            pillar_1.4.4                 
[17] RSQLite_2.2.0                 backports_1.1.7              
[19] lattice_0.20-41               glue_1.4.1                   
[21] digest_0.6.25                 promises_1.1.1               
[23] XVector_0.29.2                httpuv_1.5.4                 
[25] htmltools_0.4.0               Matrix_1.2-18                
[27] pkgconfig_2.0.3               zlibbioc_1.35.0              
[29] xtable_1.8-4                  purrr_0.3.4                  
[31] processx_3.4.2                later_1.1.0.1                
[33] tibble_3.0.1                  generics_0.0.2               
[35] ellipsis_0.3.1                withr_2.2.0                  
[37] cli_2.0.2                     mime_0.9                     
[39] magrittr_1.5                  crayon_1.3.4                 
[41] memoise_1.1.0                 ps_1.3.3                     
[43] fs_1.4.1                      fansi_0.4.1                  
[45] pkgbuild_1.0.8                tools_4.0.1                  
[47] prettyunits_1.1.1             lifecycle_0.2.0              
[49] AnnotationDbi_1.50.0          callr_3.4.3                  
[51] compiler_4.0.1                rlang_0.4.6                  
[53] grid_4.0.1                    RCurl_1.98-1.2               
[55] rstudioapi_0.11               rappdirs_0.3.1               
[57] bitops_1.0-6                  ExperimentHub_1.14.0         
[59] testthat_2.3.2                DBI_1.1.0                    
[61] curl_4.3                      R6_2.4.1                     
[63] knitr_1.28                    dplyr_1.0.0                  
[65] fastmap_1.0.1                 bit_1.1-15.2                 
[67] rprojroot_1.3-2               desc_1.2.0                   
[69] Rcpp_1.0.4.6                  vctrs_0.3.1                  
[71] dbplyr_1.4.4                  tidyselect_1.1.0             
[73] xfun_0.14

Hope this helps!

Thanks, dario

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I see.

The definition of the which generic was recently changed in BiocGenerics (in version 0.35.3, this is devel) because of a conflict with the generic defined in the Matrix package (see https://github.com/Bioconductor/BiocGenerics/issues/3). You might need to reinstall a few core packages (e.g. S4Vectors, IRanges, XVector, GenomicRanges) and possibly DelayedArray to get rid of the stale method table.

Let me know how that works.

H.

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Done, but I was already testing everything on a fresh installation.

Unfortunately, nothing changed even installing Matrix and the packages you suggested.

dario

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Oh but you are on Mac! Try to reinstall BiocGenerics, S4Vectors, IRanges, and DelayedArray from source and see if that solves the problem. If it does, I'll bump S4Vectors and IRanges versions to trigger rebuild and propagation of new binaries (a new version of DelayedArray is already on its way).

Thanks!

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It worked!

Thanks! Dario

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Good to know.

I actually don't need to bump anything. All versions were already bumped a few days ago, after which() was modified in BiocGenerics. Except for DelayedArray that I only bumped yesterday. The new DelayedArray binaries (0.15.3) should become available in a couple of hours... well maybe not the Windows one. Sigh!

H.

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