Depreciated function calls in DelayedArray

[mingl1997]

I am working on a package that uses SummarizedExperiment and am running into the following error on Ubuntu build tests:

Warning message:
replacing previous import ‘S4Arrays::makeNindexFromArrayViewport’ by ‘DelayedArray::makeNindexFromArrayViewport’ when loading ‘SummarizedExperiment’ 

In the latest Bioconductor release of DelayedArray, which I am using, the documentation notes that the function in question will be deprecated in the future in favor of the one in S4Arrays, but for the meantime, is there a workaround?

[hpages]

Please provide more details/context:

What do you mean exactly by "I am running into the following error on Ubuntu build tests"? Are you saying your package was submitted to Bioconductor and the Single Package Builder (SPB) reported the above warning? If not, please explain how you get this warning. Is it when doing R CMD INSTALL on your package, or R CMD build or R CMD check?

Do you import makeNindexFromArrayViewport explictely in your NAMESPACE? If yes, are you sure you need to import it and how do you import it?

Are you using BioC 3.17 (current release) or BioC 3.18 (current devel)?

Thanks

[mingl1997]

Hello,

I am on BioC 3.17, and this happened on R CMD check. My group recently refactored some code and this no longer comes up. Previously, this was not imported explicitly.

Thank you.

[idavydov]

I seem to be having the same message when loading SummarizedExperiment. Here's a reprex:

library(SummarizedExperiment)
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     anyDuplicated, aperm, 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:utils':
#> 
#>     findMatches
#> The following objects are masked from 'package:base':
#> 
#>     expand.grid, I, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
#> 
#>     rowMedians
#> The following objects are masked from 'package:matrixStats':
#> 
#>     anyMissing, rowMedians
#> Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
#> 'DelayedArray::makeNindexFromArrayViewport' when loading 'SummarizedExperiment'

^{Created on 2023-08-31 with reprex v2.0.2}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.0 (2023-04-21) #> os Fedora 33 (Container Image) #> system x86_64, linux-gnu #> ui X11 #> language en_US:en #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Europe/Zurich #> date 2023-08-31 #> pandoc 3.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> ! package * version date (UTC) lib source #> P abind 1.4-5 2016-07-21 [?] CRAN (R 4.3.0) #> P Biobase * 2.60.0 2023-04-25 [?] Bioconductor #> P BiocGenerics * 0.46.0 2023-04-25 [?] Bioconductor #> P bitops 1.0-7 2021-04-24 [?] CRAN (R 4.3.0) #> P cli 3.6.1 2023-03-23 [?] CRAN (R 4.3.0) #> P crayon 1.5.2 2022-09-29 [?] CRAN (R 4.3.0) #> P DelayedArray 0.26.7 2023-07-28 [?] Bioconductor #> P digest 0.6.33 2023-07-07 [?] CRAN (R 4.3.0) #> P evaluate 0.21 2023-05-05 [?] CRAN (R 4.3.0) #> P fastmap 1.1.1 2023-02-24 [?] CRAN (R 4.3.0) #> P fs 1.6.3 2023-07-20 [?] CRAN (R 4.3.0) #> P GenomeInfoDb * 1.36.2 2023-08-25 [?] Bioconductor #> P GenomeInfoDbData 1.2.10 2023-08-30 [?] Bioconductor #> P GenomicRanges * 1.52.0 2023-04-25 [?] Bioconductor #> P glue 1.6.2 2022-02-24 [?] CRAN (R 4.3.0) #> P htmltools 0.5.6 2023-08-10 [?] CRAN (R 4.3.0) #> P IRanges * 2.34.1 2023-06-22 [?] Bioconductor #> P knitr 1.43 2023-05-25 [?] CRAN (R 4.3.0) #> P lattice 0.21-8 2023-04-05 [?] CRAN (R 4.3.0) #> P lifecycle 1.0.3 2022-10-07 [?] CRAN (R 4.3.0) #> P Matrix 1.6-1 2023-08-14 [?] CRAN (R 4.3.0) #> P MatrixGenerics * 1.12.3 2023-07-30 [?] Bioconductor #> P matrixStats * 1.0.0 2023-06-02 [?] CRAN (R 4.3.0) #> P RCurl 1.98-1.12 2023-03-27 [?] CRAN (R 4.3.0) #> P reprex 2.0.2 2022-08-17 [?] CRAN (R 4.3.0) #> P rlang 1.1.1 2023-04-28 [?] CRAN (R 4.3.0) #> P rmarkdown 2.24 2023-08-14 [?] CRAN (R 4.3.0) #> P rstudioapi 0.15.0 2023-07-07 [?] CRAN (R 4.3.0) #> P S4Arrays 1.0.5 2023-07-24 [?] Bioconductor #> P S4Vectors * 0.38.1 2023-05-02 [?] Bioconductor #> P sessioninfo 1.2.2 2021-12-06 [?] CRAN (R 4.3.0) #> P SummarizedExperiment * 1.30.2 2023-06-06 [?] Bioconductor #> P withr 2.5.0 2022-03-03 [?] CRAN (R 4.3.0) #> P xfun 0.40 2023-08-09 [?] CRAN (R 4.3.0) #> P XVector 0.40.0 2023-04-25 [?] Bioconductor #> P yaml 2.3.7 2023-01-23 [?] CRAN (R 4.3.0) #> P zlibbioc 1.46.0 2023-04-25 [?] Bioconductor #> #> ... #> #> P ── Loaded and on-disk path mismatch. #> #> ────────────────────────────────────────────────────────────────────────────── ```

[hpages]

How do you install your packages?

Can you try to reinstall S4Arrays, DelayedArray, and SummarizedExperiment, with:

BiocManager::install(c("S4Arrays", "DelayedArray", "SummarizedExperiment"), force=TRUE)

Then quit R, and try library(SummarizedExperiment) again in a fresh R session.