Bioconductor package outdated

[qhmu]

Dear LTLA,

Thanks for creating this package which looks really fascinating!

We installed this package via BiocManager::install("scRNAseq") and it can be loaded without any problem via library(scRNAseq) so the installation is successful.

However, when I try to load the MacoskoRetinaData() dataset from the package, it says Error in MacoskoRetinaData() : could not find function "MacoskoRetinaData"

I then checked the package information, and I found it seems to be outdated, because was compiled in Dec 2018, which is about 1 year ago. I also checked the functions within this package, but I only saw these below:

Description Gene-level read counts of three public scRNA-seq datasets. See vignette for details. Details This package contains a collection of three publicly available single-cell RNA-seq datasets. The dataset fluidigm contains 65 cells from Pollen et al. (2014), each sequenced at high and low coverage. The dataset th2 contains 96 T helper cells from Mahata et al. (2014). The dataset allen contains 379 cells from the mouse visual cortex. This is a subset of the data published in Tasic et al. (2016).

See the package vignette for details on the pre-processing of the data.

Could you please suggest how I should install or update this package? Thanks!

SessionInfo: sessionInfo()

R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/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] scRNAseq_1.8.0 SingleCellExperiment_1.4.1 SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.6
[6] matrixStats_0.55.0 Biobase_2.42.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2 IRanges_2.16.0
[11] S4Vectors_0.20.1 BiocGenerics_0.28.0 devtools_2.2.1 usethis_1.5.1
loaded via a namespace (and not attached): [1] Rcpp_1.0.3 XVector_0.22.0 compiler_3.5.3 zlibbioc_1.28.0 prettyunits_1.0.2 bitops_1.0-6
[7] remotes_2.1.0 tools_3.5.3 testthat_2.2.1 digest_0.6.23 pkgbuild_1.0.6 pkgload_1.0.2
[13] lattice_0.20-38 memoise_1.1.0 rlang_0.4.2 Matrix_1.2-17 cli_1.1.0 rstudioapi_0.10
[19] curl_4.3 yaml_2.2.0 GenomeInfoDbData_1.2.0 withr_2.1.2 desc_1.2.0 fs_1.3.1
[25] grid_3.5.3 rprojroot_1.3-2 glue_1.3.1 R6_2.4.1 processx_3.4.1 sessioninfo_1.1.1
[31] callr_3.3.2 magrittr_1.5 backports_1.1.5 ps_1.3.0 ellipsis_0.3.0 assertthat_0.2.1
[37] RCurl_1.95-4.12 crayon_1.3.4

[LTLA]

Seems like you need R 3.6.+ with Bioconductor 3.10, see here.

[qhmu]

Great! Updating R and Bioconductor solved the issue. Thanks.