SingleR: download Error

[isaiao01]

Hi everyone,

I have downloaded SingleR using biocmanager and i am attempting to load it in using the library function. However, i keep getting this error:

Warning: package ‘SingleR’ was built under R version 4.3.2Error: package or namespace load failed for ‘SingleR’: object ‘initializeCpp’ is not exported by 'namespace:beachmat'

I have attempted to restart R and even download the package using a zip file but nothing is working. Help!

[j-andrews7]

I expect your package versions are not consistent for a given Bioconductor release. What does BiocManager::valid() yield? More than likely, it'll tell you that you have version mismatches, which is likely the cause of this issue.

[isaiao01]

This is what i yield loading BiocManager: : valid()

BiocManager::valid() 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: http://cran.rstudio.com/

• sessionInfo()

R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8

time zone: America/Chicago tzcode source: internal

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] miQC_1.8.0 scCustomize_2.0.1 UCell_2.4.0 lubridate_1.9.3
[5] forcats_1.0.0 stringr_1.5.1 purrr_1.0.2 readr_2.1.4
[9] tibble_3.2.1 tidyverse_2.0.0 openxlsx_4.2.5.2 RColorBrewer_1.1-3
[13] SeuratWrappers_0.3.1 ggplot2_3.5.0.9000 reshape2_1.4.4 tidyr_1.3.0
[17] Matrix_1.6-1.1 R.utils_2.12.2 R.oo_1.25.0 R.methodsS3_1.8.2
[21] patchwork_1.2.0.9000 Seurat_5.0.0 SeuratObject_5.0.0 sp_2.0-0
[25] dplyr_1.1.3 celldex_1.12.0 Rcpp_1.0.11 monocle3_1.4.5
[29] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2 Biobase_2.60.0 GenomicRanges_1.52.1
[33] GenomeInfoDb_1.36.4 IRanges_2.34.1 S4Vectors_0.38.2 BiocGenerics_0.46.0
[37] MatrixGenerics_1.14.0 matrixStats_1.0.0

loaded via a namespace (and not attached): [1] spatstat.sparse_3.0-2 bitops_1.0-7 httr_1.4.7
[4] tools_4.3.1 sctransform_0.4.1 utf8_1.2.3
[7] R6_2.5.1 lazyeval_0.2.2 uwot_0.1.16
[10] withr_3.0.0 gridExtra_2.3 progressr_0.14.0
[13] cli_3.6.1 pacman_0.5.1 spatstat.explore_3.2-3
[16] fastDummies_1.7.3 spatstat.data_3.0-4 ggridges_0.5.6
[19] pbapply_1.7-2 parallelly_1.37.1 rstudioapi_0.16.0
[22] RSQLite_2.3.1 shape_1.4.6.1 generics_0.1.3
[25] ica_1.0-3 spatstat.random_3.1-6 zip_2.3.0
[28] ggbeeswarm_0.7.2 fansi_1.0.4 abind_1.4-5
[31] lifecycle_1.0.4 yaml_2.3.7 snakecase_0.11.1
[34] BiocFileCache_2.10.2 Rtsne_0.16 paletteer_1.6.0
[37] grid_4.3.1 blob_1.2.4 promises_1.2.1
[40] ExperimentHub_2.10.0 crayon_1.5.2 miniUI_0.1.1.1
[43] lattice_0.22-6 beachmat_2.16.0 cowplot_1.1.3
[46] KEGGREST_1.40.1 pillar_1.9.0 knitr_1.45
[49] boot_1.3-30 future.apply_1.11.2 codetools_0.2-20
[52] leiden_0.4.3.1 glue_1.6.2 data.table_1.14.8
[55] remotes_2.5.0 vctrs_0.6.3 png_0.1-8
[58] spam_2.10-0 gtable_0.3.5 rematch2_2.1.2
[61] cachem_1.0.8 xfun_0.40 S4Arrays_1.0.6
[64] mime_0.12 survival_3.6-4 interactiveDisplayBase_1.40.0 [67] fitdistrplus_1.1-11 ROCR_1.0-11 nlme_3.1-164
[70] bit64_4.0.5 filelock_1.0.2 RcppAnnoy_0.0.21
[73] irlba_2.3.5.1 vipor_0.4.7 KernSmooth_2.23-24
[76] colorspace_2.1-0 DBI_1.2.2 nnet_7.3-19
[79] ggrastr_1.0.2 tidyselect_1.2.1 bit_4.0.5
[82] compiler_4.3.1 curl_5.1.0 BiocNeighbors_1.18.0
[85] DelayedArray_0.26.7 plotly_4.10.4 scales_1.3.0
[88] lmtest_0.9-40 rappdirs_0.3.3 digest_0.6.33
[91] goftest_1.2-3 spatstat.utils_3.0-3 minqa_1.2.6
[94] rmarkdown_2.27 XVector_0.40.0 htmltools_0.5.6.1
[97] pkgconfig_2.0.3 lme4_1.1-34 sparseMatrixStats_1.14.0
[100] dbplyr_2.5.0 fastmap_1.1.1 GlobalOptions_0.1.2
[103] rlang_1.1.1 htmlwidgets_1.6.2 shiny_1.8.1.1
[106] DelayedMatrixStats_1.22.6 zoo_1.8-12 jsonlite_1.8.7
[109] BiocParallel_1.34.2 BiocSingular_1.16.0 RCurl_1.98-1.12
[112] magrittr_2.0.3 modeltools_0.2-23 GenomeInfoDbData_1.2.11
[115] dotCall64_1.1-0 munsell_0.5.1 reticulate_1.34.0
[118] stringi_1.7.12 zlibbioc_1.46.0 MASS_7.3-60
[121] flexmix_2.3-19 AnnotationHub_3.10.1 plyr_1.8.9
[124] parallel_4.3.1 listenv_0.9.1 ggrepel_0.9.4
[127] deldir_1.0-9 Biostrings_2.68.1 splines_4.3.1
[130] tensor_1.5 circlize_0.4.16 hms_1.1.3
[133] igraph_1.5.1 spatstat.geom_3.2-5 RcppHNSW_0.5.0
[136] ScaledMatrix_1.8.1 BiocVersion_3.18.1 evaluate_0.23
[139] BiocManager_1.30.22 ggprism_1.0.5 nloptr_2.0.3
[142] tzdb_0.4.0 httpuv_1.6.12 RANN_2.6.1
[145] polyclip_1.10-6 future_1.33.2 scattermore_1.2
[148] janitor_2.2.0 rsvd_1.0.5 xtable_1.8-4
[151] RSpectra_0.16-1 later_1.3.1 viridisLite_0.4.2
[154] memoise_2.0.1 beeswarm_0.4.0 AnnotationDbi_1.64.1
[157] cluster_2.1.6 timechange_0.2.0 globals_0.16.3

Bioconductor version '3.18'

• 140 packages out-of-date
• 1 packages too new

create a valid installation with

BiocManager::install(c( "beachmat", "Biobase", "BiocGenerics", "BiocManager", "BiocNeighbors", "BiocParallel", "BiocSingular", "Biostrings", "bslib", "cachem", "Cairo", "cli", "curl", "data.table", "DelayedArray", "DelayedMatrixStats", "deldir", "digest", "dotCall64", "dplyr", "fansi", "fastmap", "filelock", "gdtools", "GenomeInfoDb", "GenomicRanges", "gert", "ggplot2", "ggrepel", "ggsci", "glue", "gplots", "gtools", "HDF5Array", "htmltools", "htmlwidgets", "httpuv", "igraph", "IHW", "impute", "infercnv", "IRanges", "jsonlite", "KEGGgraph", "KEGGREST", "knitr", "later", "leidenbase", "limma", "lme4", "lpsymphony", "matrixStats", "minqa", "miQC", "monocle", "MsCoreUtils", "MSnbase", "msqrob2", "MultiAssayExperiment", "multtest", "mvtnorm", "mzID", "mzR", "Nebulosa", "openssl", "org.Hs.eg.db", "org.Mm.eg.db", "patchwork", "pathview", "pcaMethods", "PCAtools", "preprocessCore", "promises", "ProtGenerics", "QFeatures", "qvalue", "R.oo", "R.utils", "ragg", "RBGL", "Rcpp", "RcppAnnoy", "RcppHNSW", "RCurl", "reactome.db", "ReactomePA", "readr", "ResidualMatrix", "reticulate", "Rgraphviz", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rJava", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "Rtsne", "RUVSeq", "s2", "S4Arrays", "S4Vectors", "ScaledMatrix", "scCustomize", "scuttle", "Seurat", "SeuratObject", "sf", "ShortRead", "SingleCellExperiment", "sp", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.utils", "stringi", "SummarizedExperiment", "systemfonts", "textshaping", "tidygraph", "tidyr", "timechange", "treeio", "UCell", "UniProt.ws", "utf8", "uwot", "VariantAnnotation", "vctrs", "venneuler", "vsn", "xfun", "XML", "xml2", "XVector", "yaml", "zip", "zlibbioc" ), update = TRUE, ask = FALSE, force = TRUE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message: 140 packages out-of-date; 1 packages too new

[j-andrews7]

Well, there's your answer.

[isaiao01]

So,

does that mean I have to downgrade my Biocmanager version to 3.17 or upgrade?

[j-andrews7]

Package versions need to be consistent for the Bioconductor release. Both of the 3.18 and 3.17 Bioconductor releases are designed to work with R 4.3.x, so the choice of which to use is up to you. Upgrading is probably easiest since it provides the command for you to do so.