Error in rowData(object)

[ONeillMB1]

I just updated several Bioconductor packages for scRNA-seq analysis (SingleCellExperiment, simpleSingleCell, scran, scater..) and am now having an issue with the SingleCellExperiment class that breaks most downstream functions.

Error in rowData(object) : could not find symbol "use.names" in environment of the generic function

I have replicated the error with both my own data as well as made-up data so this appears to be an issue in the class and not with the reading-in of the data.

For reference, I was using the read10xCounts {DropletUtils} function to read in my data. For the made-up data I simply ran the following: library(SingleCellExperiment) counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10) sce <- SingleCellExperiment(assays = list(counts = counts)) sce

Here is my session info:

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] bindrcpp_0.2.2 usethis_1.4.0 devtools_2.0.1 stringr_1.3.1
[5] simpleSingleCell_1.4.1 TENxBrainData_1.2.0 HDF5Array_1.8.0 rhdf5_2.24.0
[9] BiocNeighbors_1.0.0 BiocFileCache_1.6.0 dbplyr_1.2.2 DropletUtils_1.2.2
[13] scRNAseq_1.8.0 TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0 GenomicFeatures_1.32.0 cluster_2.0.7-1
[17] dynamicTreeCut_1.63-1 pheatmap_1.0.10 scran_1.10.2 org.Mm.eg.db_3.6.0
[21] AnnotationDbi_1.42.1 scater_1.10.1 ggplot2_3.1.0 SingleCellExperiment_1.4.1
[25] SummarizedExperiment_1.12.0 DelayedArray_0.6.0 matrixStats_0.53.1 Biobase_2.40.0
[29] GenomicRanges_1.34.0 GenomeInfoDb_1.16.0 IRanges_2.16.0 S4Vectors_0.20.1
[33] BiocGenerics_0.26.0 gdata_2.18.0 readxl_1.1.0 destiny_2.12.0
[37] mvoutlier_2.0.9 sgeostat_1.0-27 Rtsne_0.14 BiocParallel_1.14.1
[41] knitr_1.20 BiocStyle_2.10.0 Seurat_3.0.0.9000 edgeR_3.22.5
[45] limma_3.36.5

loaded via a namespace (and not attached): [1] rappdirs_0.3.1 rtracklayer_1.40.3 ggthemes_4.0.1 prabclus_2.2-6 GGally_1.4.0
[6] R.methodsS3_1.7.1 pkgmaker_0.27.2 tidyr_0.8.1 bit64_0.9-7 irlba_2.3.2
[11] R.utils_2.6.0 data.table_1.11.8 RCurl_1.95-4.10 metap_0.9 callr_3.1.1
[16] cowplot_0.9.4 RSQLite_2.1.1 RANN_2.5.1 proxy_0.4-22 future_1.11.1.1
[21] bit_1.1-14 httpuv_1.4.3 assertthat_0.2.0 viridis_0.5.1 hms_0.4.2
[26] promises_1.0.1 evaluate_0.10.1 DEoptimR_1.0-8 progress_1.1.2 caTools_1.17.1
[31] igraph_1.1.0 DBI_1.0.0 htmlwidgets_1.2 reshape_0.8.8 purrr_0.2.5
[36] dplyr_0.7.6 backports_1.1.2 trimcluster_0.1-2 sROC_0.1-2 biomaRt_2.36.1
[41] remotes_2.0.2 TTR_0.23-4 ROCR_1.0-7 abind_1.4-5 RcppEigen_0.3.3.4.0
[46] withr_2.1.2 robustbase_0.93-0 vcd_1.4-4 GenomicAlignments_1.16.0 xts_0.11-2
[51] prettyunits_1.0.2 mclust_5.4 ExperimentHub_1.8.0 ape_5.1 lazyeval_0.2.1
[56] crayon_1.3.4 laeken_0.5.0 pkgconfig_2.0.2 zCompositions_1.1.2 pkgload_1.0.2
[61] nlme_3.1-137 vipor_0.4.5 nnet_7.3-12 bindr_0.1.1 rlang_0.2.1
[66] globals_0.12.4 diptest_0.75-7 pls_2.7-0 registry_0.5 rsvd_0.9
[71] AnnotationHub_2.14.3 cellranger_1.1.0 rprojroot_1.3-2 lmtest_0.9-36 rngtools_1.3.1
[76] Matrix_1.2-14 carData_3.0-1 Rhdf5lib_1.2.1 boot_1.3-20 zoo_1.8-1
[81] beeswarm_0.2.3 processx_3.2.1 ggridges_0.5.0 png_0.1-7 viridisLite_0.3.0
[86] bitops_1.0-6 R.oo_1.22.0 KernSmooth_2.23-15 Biostrings_2.48.0 blob_1.1.1
[91] DelayedMatrixStats_1.2.0 scales_0.5.0 memoise_1.1.0 magrittr_1.5 plyr_1.8.4
[96] ica_1.0-2 gplots_3.0.1 bibtex_0.4.2 zlibbioc_1.26.0 compiler_3.5.0
[101] RColorBrewer_1.1-2 rrcov_1.4-4 fitdistrplus_1.0-9 cli_1.0.0 Rsamtools_1.32.0
[106] XVector_0.20.0 listenv_0.7.0 ps_1.3.0 pbapply_1.3-4 Formula_1.2-3
[111] MASS_7.3-50 tidyselect_0.2.4 stringi_1.2.4 forcats_0.3.0 yaml_2.1.19
[116] locfit_1.5-9.1 ggrepel_0.8.0 grid_3.5.0 tools_3.5.0 future.apply_1.1.0
[121] rio_0.5.10 rstudioapi_0.7 foreign_0.8-70 gridExtra_2.3 smoother_1.1
[126] scatterplot3d_0.3-41 digest_0.6.15 BiocManager_1.30.4 shiny_1.1.0 fpc_2.1-11
[131] Rcpp_1.0.0 car_3.0-2 SDMTools_1.1-221 later_0.7.2 httr_1.3.1
[136] csSAM_1.4 kernlab_0.9-26 colorspace_1.3-2 fs_1.2.6 XML_3.98-1.11
[141] reticulate_1.7 truncnorm_1.0-8 splines_3.5.0 statmod_1.4.30 sp_1.3-1
[146] flexmix_2.3-14 sessioninfo_1.1.1 plotly_4.7.1 xtable_1.8-2 jsonlite_1.5
[151] testthat_2.0.1 modeltools_0.2-21 R6_2.2.2 NADA_1.6-1 mime_0.5
[156] pillar_1.2.3 htmltools_0.3.6 glue_1.3.0 VIM_4.7.0 cvTools_0.3.2
[161] interactiveDisplayBase_1.20.0 class_7.3-14 codetools_0.2-15 pkgbuild_1.0.2 tsne_0.1-3
[166] pcaPP_1.9-73 mvtnorm_1.0-8 lattice_0.20-35 tibble_1.4.2 curl_3.2
[171] ggbeeswarm_0.6.0 gtools_3.5.0 zip_1.0.0 openxlsx_4.1.0 survival_2.42-3
[176] rmarkdown_1.9 desc_1.2.0 munsell_0.4.3 e1071_1.7-0 GenomeInfoDbData_1.1.0
[181] haven_1.1.2 reshape2_1.4.3 gtable_0.2.0 robCompositions_2.0.9

[ONeillMB1]

It seems it was some incompatibility with another package. Resolved.

[LTLA]

Probably best to run BiocManager::valid() if you haven't already.

[hrkg52]

It seems it was some incompatibility with another package. Resolved.

Hello. Could you please explain how you solved the problem ? I encounter the same issue and I cannot find the source.

[LTLA]

Please open a new issue with a minimal working example and session information.

[mahsayazdani]

I had the same issue and I solved it by reinstalling the package that caused this error.