error when loading the package

[lixin4306ren]

I installed the muscat with Bioconductor version 3.12 and R 4.0.0 without error but got following error when loading it.

> BiocManager::install("muscat")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'muscat'
trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/macosx/contrib/4.0/muscat_1.3.0.tgz'
Content type 'application/x-gzip' length 4290963 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

The downloaded binary packages are in
    /var/folders/wn/5wyp_69d36b50ypsrc8w5nn40000gn/T//RtmpedkOw3/downloaded_packages
Old packages: 'ape', 'BSgenome.Hsapiens.UCSC.hg38', 'destiny', 'haven', 'mnormt', 'rms'
Update all/some/none? [a/s/n]: 
n
> library(muscat)
Error: package or namespace load failed for ‘muscat’:
 object ‘computeLibraryFactors’ is not exported by 'namespace:scater'

[HelenaLC]

Could you please attach the output of sessionInfo()?

[lixin4306ren]

Could you please attach the output of sessionInfo()?

sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] nlme_3.1-148 bitops_1.0-6 matrixStats_0.56.0
[4] bit64_0.9-7 RColorBrewer_1.1-2 progress_1.2.2
[7] GenomeInfoDb_1.25.1 numDeriv_2016.8-1.1 tools_4.0.0
[10] TMB_1.7.16 irlba_2.3.3 R6_2.4.1
[13] vipor_0.4.5 DBI_1.1.0 BiocGenerics_0.35.3
[16] colorspace_1.4-1 GetoptLong_0.1.8 gridExtra_2.3
[19] tidyselect_1.1.0 prettyunits_1.1.1 DESeq2_1.29.4
[22] bit_1.1-15.2 compiler_4.0.0 Biobase_2.49.0
[25] BiocNeighbors_1.7.0 DelayedArray_0.15.1 scales_1.1.1
[28] genefilter_1.71.0 blme_1.0-4 digest_0.6.25
[31] minqa_1.2.4 XVector_0.29.1 scater_1.17.1
[34] pkgconfig_2.0.3 lme4_1.1-23 limma_3.45.0
[37] rlang_0.4.6 GlobalOptions_0.1.1 rstudioapi_0.11
[40] RSQLite_2.2.0 DelayedMatrixStats_1.11.0 shape_1.4.4
[43] generics_0.0.2 BiocParallel_1.23.0 dplyr_1.0.0
[46] BiocSingular_1.5.0 RCurl_1.98-1.2 magrittr_1.5
[49] GenomeInfoDbData_1.2.3 scuttle_0.99.8 Matrix_1.2-18
[52] ggbeeswarm_0.6.0 Rcpp_1.0.4.6 munsell_0.5.0
[55] S4Vectors_0.27.11 viridis_0.5.1 lifecycle_0.2.0
[58] yaml_2.2.1 edgeR_3.31.3 MASS_7.3-51.6
[61] SummarizedExperiment_1.19.4 zlibbioc_1.35.0 grid_4.0.0
[64] blob_1.2.1 parallel_4.0.0 crayon_1.3.4
[67] lattice_0.20-41 splines_4.0.0 annotate_1.67.0
[70] circlize_0.4.9 hms_0.5.3 locfit_1.5-9.4
[73] ComplexHeatmap_2.5.3 pillar_1.4.4 GenomicRanges_1.41.3
[76] boot_1.3-25 rjson_0.2.20 geneplotter_1.67.0
[79] stats4_4.0.0 XML_3.99-0.3 glue_1.4.1
[82] data.table_1.12.8 png_0.1-7 vctrs_0.3.0
[85] nloptr_1.2.2.1 gtable_0.3.0 purrr_0.3.4
[88] clue_0.3-57 ggplot2_3.3.1 rsvd_1.0.3
[91] xtable_1.8-4 viridisLite_0.3.0 survival_3.1-12
[94] SingleCellExperiment_1.11.2 tibble_3.0.1 lmerTest_3.1-2
[97] glmmTMB_1.0.1 beeswarm_0.2.3 AnnotationDbi_1.51.0
[100] memoise_1.1.0 IRanges_2.23.7 cluster_2.1.0
[103] statmod_1.4.34 ellipsis_0.3.1

[HelenaLC]

Before looking into this- I notice that you're using Bioc 3.12 (the development version)- is this intended?

[csoneson]

I think this is due to problems with re-exporting in scater 1.17.1 (see https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016846.html) - should clear up today or tomorrow with 1.17.2.

[lixin4306ren]

@csoneson, thank you. I think that's the reason. I will update scater package and try muscat later.

[HelenaLC]

Please keep me posted so I can look into it or close the issue if it resolves itself :)