PeteHaitch
commented
6 months ago Please provide a reproducible example (as text and not as a screenshot).
E.g., this demonstrates SingleR() working on my machine:
suppressPackageStartupMessages(library(SingleR))
# Mocking up data with log-normalized expression values:
ref <- .mockRefData()
test <- .mockTestData(ref)
ref <- scuttle::logNormCounts(ref)
test <- scuttle::logNormCounts(test)
# Running the classification with different options:
SingleR(test, ref, labels=ref$label)
#> DataFrame with 100 rows and 4 columns
#> scores labels delta.next pruned.labels
#> <matrix> <character> <numeric> <character>
#> 1 -0.0147788:0.0264488:0.12898508:... C 0.1025363 C
#> 2 -0.0104899:0.0331671:0.00738906:... E 0.0910800 E
#> 3 0.0249717:0.0408587:0.00203195:... D 0.0521095 D
#> 4 0.1014052:0.0373862:0.02674975:... A 0.0640189 A
#> 5 -0.0240772:0.0175876:0.01874797:... E 0.0719095 E
#> ... ... ... ... ...
#> 96 0.0499047: 0.02929928:0.0657537:... D 0.0969816 D
#> 97 0.0202227: 0.00763344:0.0447376:... D 0.1166725 D
#> 98 0.0642006: 0.01908204:0.0228159:... A 0.0144964 A
#> 99 0.0251169: 0.03410851:0.1065300:... C 0.0724215 C
#> 100 0.0325325:-0.01377622:0.0302404:... D 0.0547933 DPlease also provide the output of BiocManager::valid() and sessionInfo(), e.g.,
BiocManager::valid()
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#> CRAN: https://cran.rstudio.com/
#> [1] TRUE
sessionInfo()
#> R Under development (unstable) (2023-10-28 r85429)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Ventura 13.6.1
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> time zone: Australia/Melbourne
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] SingleR_2.5.0 SummarizedExperiment_1.33.1
#> [3] Biobase_2.63.0 GenomicRanges_1.55.1
#> [5] GenomeInfoDb_1.39.1 IRanges_2.37.0
#> [7] S4Vectors_0.41.2 BiocGenerics_0.49.1
#> [9] MatrixGenerics_1.15.0 matrixStats_1.2.0
#>
#> loaded via a namespace (and not attached):
#> [1] SparseArray_1.3.1 bitops_1.0-7
#> [3] scuttle_1.13.0 lattice_0.22-5
#> [5] digest_0.6.33 evaluate_0.23
#> [7] sparseMatrixStats_1.15.0 grid_4.4.0
#> [9] fastmap_1.1.1 Matrix_1.6-4
#> [11] BiocManager_1.30.22 SingleCellExperiment_1.25.0
#> [13] codetools_0.2-19 abind_1.4-5
#> [15] cli_3.6.2 rlang_1.1.2
#> [17] crayon_1.5.2 XVector_0.43.0
#> [19] reprex_2.0.2 withr_2.5.2
#> [21] DelayedArray_0.29.0 yaml_2.3.8
#> [23] S4Arrays_1.3.1 tools_4.4.0
#> [25] beachmat_2.19.0 parallel_4.4.0
#> [27] BiocParallel_1.37.0 GenomeInfoDbData_1.2.11
#> [29] rsvd_1.0.5 lifecycle_1.0.4
#> [31] zlibbioc_1.49.0 BiocSingular_1.19.0
#> [33] fs_1.6.3 irlba_2.3.5.1
#> [35] ScaledMatrix_1.11.0 glue_1.6.2
#> [37] Rcpp_1.0.11 xfun_0.41
#> [39] rstudioapi_0.15.0 knitr_1.45
#> [41] htmltools_0.5.7 rmarkdown_2.25
#> [43] DelayedMatrixStats_1.25.1 compiler_4.4.0
#> [45] RCurl_1.98-1.13
LeaLe88
dviraran
Dear all,
Suddenly I am getting the following error:
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.when running the SingleR with
I did not get this error before. I have been installing some new packages today / updates. What can I do now?
Thank you very much!