Can't install monocle3 in 4.2.1 R on Windows

Question

trying to download monocle3: https://cole-trapnell-lab.github.io/monocle3/docs/installation/

receiving the error:

Installing package into ‘C:/Users/drnan/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
ERROR: dependency 'Matrix.utils' is not available for package 'monocle3'
* removing 'C:/Users/drnan/AppData/Local/R/win-library/4.2/monocle3'
  installation of package ‘C:/Users/drnan/AppData/Lo

cal/Temp/RtmpEl0M3e/file17d832b82f61/monocle3_1.2.9.tar.gz’ had non-zero exit status

I also received an error for line: BiocManager::install(version = "3.14")

Error: Bioconductor version '3.14' requires R version '4.1'; use `BiocManager::install(version = '3.15')` with R version 4.2; see https://bioconductor.org/install

With version 3.15, however Matrix.utils wouldn't install:
BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'lme4', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment', 'batchelor', 'Matrix.utils',
                       'HDF5Array', 'terra', 'ggrastr'))

Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'BiocGenerics' 'DelayedArray' 'DelayedMatrixStats' 'limma' 'lme4'
  'S4Vectors' 'SingleCellExperiment' 'SummarizedExperiment' 'batchelor' 'HDF5Array' 'terra' 'ggrastr' 
2: packages ‘TRUE’, ‘Matrix.utils’ are not available for Bioconductor version '3.15'

so my question is, what are the right compatible versions of BIoconductor, Monocle3, with R 4.2.1? I don't even need Bioc, just need Monocle3. Completely blocked!!! HELP!!!

Answer 1

I just solved this issue on my local computer. So the whole reason why the installation failed is because of Matrix.utils not available (there is even notification in cran https://cran.r-project.org/web/packages/Matrix.utils/index.html that it is removed because "issues were not corrected despite reminders".)

Solution for mac os x:

• download Matrix.utils_0.9.8.tgz from https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.5/Matrix.utils_0.9.8.tgz (please find the windows alternative, perhaps it is found in https://cran.r-project.org/src/contrib/Archive/Matrix.utils/)
• install using install.packages("locationfolder/Matrix.utils_0.9.8.tgz", repos = NULL, type="source")
• rerun devtools::install_github('cole-trapnell-lab/monocle3')
• test with library(monocle3)

Hope this helps!