Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'

[njtourtillott]

Hi, I have been having trouble using singleR. Every time I try to execute the singleR function I get this error and am uncertain what is causing this issue.

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7 (However, I get the same error from the same code when run on windows 10 through AWS)

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding

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] sctransform_0.3.2 SingleR_1.6.1
[3] celldex_1.2.0 scDblFinder_1.6.0
[5] scater_1.20.1 scuttle_1.2.0
[7] SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0
[9] Biobase_2.52.0 GenomicRanges_1.44.0
[11] GenomeInfoDb_1.28.1 IRanges_2.26.0
[13] S4Vectors_0.30.0 BiocGenerics_0.38.0
[15] MatrixGenerics_1.4.0 matrixStats_0.59.0
[17] ggplot2_3.3.5 patchwork_1.1.1
[19] SeuratObject_4.0.2 Seurat_4.0.3
[21] dplyr_1.0.7

loaded via a namespace (and not attached):
[1] utf8_1.2.1 reticulate_1.20
[3] tidyselect_1.1.1 RSQLite_2.2.7
[5] AnnotationDbi_1.54.1 htmlwidgets_1.5.3
[7] grid_4.1.0 BiocParallel_1.26.1
[9] Rtsne_0.15 munsell_0.5.0
[11] ScaledMatrix_1.0.0 codetools_0.2-18
[13] ica_1.0-2 statmod_1.4.36
[15] scran_1.20.1 xgboost_1.4.1.1
[17] future_1.21.0 miniUI_0.1.1.1
[19] withr_2.4.2 argparse_2.0.3
[21] colorspace_2.0-2 filelock_1.0.2
[23] ROCR_1.0-11 tensor_1.5
[25] listenv_0.8.0 labeling_0.4.2
[27] GenomeInfoDbData_1.2.6 polyclip_1.10-0
[29] farver_2.1.0 bit64_4.0.5
[31] TH.data_1.0-10 coda_0.19-4
[33] parallelly_1.26.1 vctrs_0.3.8
[35] generics_0.1.0 lambda.r_1.2.4
[37] BiocFileCache_2.0.0 fastcluster_1.2.3
[39] doParallel_1.0.16 R6_2.5.0
[41] ggbeeswarm_0.6.0 rsvd_1.0.5
[43] locfit_1.5-9.4 reshape_0.8.8
[45] bitops_1.0-7 spatstat.utils_2.2-0
[47] cachem_1.0.5 DelayedArray_0.18.0
[49] assertthat_0.2.1 promises_1.2.0.1
[51] scales_1.1.1 multcomp_1.4-17
[53] beeswarm_0.4.0 gtable_0.3.0
[55] beachmat_2.8.0 globals_0.14.0
[57] goftest_1.2-2 sandwich_3.0-1
[59] rlang_0.4.11 splines_4.1.0
[61] lazyeval_0.2.2 spatstat.geom_2.2-0
[63] BiocManager_1.30.16 yaml_2.2.1
[65] reshape2_1.4.4 abind_1.4-5
[67] httpuv_1.6.1 tools_4.1.0
[69] gplots_3.1.1 ellipsis_0.3.2
[71] spatstat.core_2.2-0 RColorBrewer_1.1-2
[73] phyclust_0.1-30 ggridges_0.5.3
[75] Rcpp_1.0.7 plyr_1.8.6
[77] sparseMatrixStats_1.4.0 zlibbioc_1.38.0
[79] purrr_0.3.4 RCurl_1.98-1.3
[81] rpart_4.1-15 deldir_0.2-10
[83] pbapply_1.4-3 viridis_0.6.1
[85] cowplot_1.1.1 zoo_1.8-9
[87] ggrepel_0.9.1 cluster_2.1.2
[89] magrittr_2.0.1 futile.options_1.0.1
[91] data.table_1.14.0 scattermore_0.7
[93] lmtest_0.9-38 RANN_2.6.1
[95] mvtnorm_1.1-2 fitdistrplus_1.1-5
[97] mime_0.11 xtable_1.8-4
[99] gridExtra_2.3 compiler_4.1.0
[101] tibble_3.1.2 KernSmooth_2.23-20
[103] crayon_1.4.1 htmltools_0.5.1.1
[105] mgcv_1.8-36 later_1.2.0
[107] libcoin_1.0-8 tidyr_1.1.3
[109] DBI_1.1.1 formatR_1.11
[111] ExperimentHub_2.0.0 dbplyr_2.1.1
[113] MASS_7.3-54 rappdirs_0.3.3
[115] Matrix_1.3-4 metapod_1.0.0
[117] igraph_1.2.6 pkgconfig_2.0.3
[119] coin_1.4-1 plotly_4.9.4.1
[121] spatstat.sparse_2.0-0 foreach_1.5.1
[123] vipor_0.4.5 dqrng_0.3.0
[125] XVector_0.32.0 stringr_1.4.0
[127] digest_0.6.27 RcppAnnoy_0.0.18
[129] spatstat.data_2.1-0 Biostrings_2.60.1
[131] leiden_0.3.8 uwot_0.1.10
[133] edgeR_3.34.0 DelayedMatrixStats_1.14.0
[135] curl_4.3.2 gtools_3.9.2
[137] modeltools_0.2-23 shiny_1.6.0
[139] lifecycle_1.0.0 nlme_3.1-152
[141] jsonlite_1.7.2 BiocNeighbors_1.10.0
[143] futile.logger_1.4.3 viridisLite_0.4.0
[145] limma_3.48.1 fansi_0.5.0
[147] pillar_1.6.1 lattice_0.20-44
[149] KEGGREST_1.32.0 fastmap_1.1.0
[151] httr_1.4.2 survival_3.2-11
[153] interactiveDisplayBase_1.30.0 glue_1.4.2
[155] iterators_1.0.13 png_0.1-7
[157] bluster_1.2.1 BiocVersion_3.13.1
[159] bit_4.0.4 stringi_1.6.2
[161] blob_1.2.1 BiocSingular_1.8.1
[163] AnnotationHub_3.0.1 caTools_1.18.2
[165] memoise_2.0.0 ape_5.5
[167] irlba_2.3.3 future.apply_1.7.0

[MubasherMohammed]

Hi, did you manage to solve this?
Thanks..

[kristifourie]

Hi, I am running singleR and also get this issue. How did you solve it?

[aleferna]

same here

[dviraran]

This repo is not maintained. Please raise issues @ https://github.com/LTLA/SingleR