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ChenWeiyan / LandSCENT

Landscape Single Cell Entropy
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install #1

Closed AMaynard10 closed 5 years ago

AMaynard10 commented 5 years ago

Hello, maybe I missed it but how do you install the package?

AMaynard10 commented 5 years ago

library(devtools) install_github("ChenWeiyan/LandSCENT")

The above worked for install, however there is a dependent package error:

No methods found in package ‘DelayedArray’ for request: ‘write_block_to_sink’ when loading ‘DelayedMatrixStats’

I tried then to install the package alone and found the package is not available for R 3.5.0.

install.packages("DelayedArray") package ‘DelayedArray’ is not available (for R version 3.5.0)

ChenWeiyan commented 5 years ago

Hello,

I think it is about the installation of package DelayedArray. Since DelayedArray is a Bioconductor package, install_github may not correctly install it before loading DelayedMatrixStats.

The proper way to install it is the following:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DelayedArray")

Another way may solve the problem is, run the following before install LandSCENT:

BiocManager::install(c("DelayedArray", "scater", "cluster", "corpcor", "igraph", "isva", "mclust", "parallel", "stats", "grDevices", "graphics", "marray", "scater", "Biobase", "SingleCellExperiment", "Rtsne", "irlba", "plot3D", "MASS", "dbscan", "monocle", "DelayedArray", "Matrix"))

In case you get other packages which are not well installed.

BTW, I recommend using BiocManager:install to install packages, which can deal with packages both from CRAN and Bioconductor.

Hope this be helpful!

AMaynard10 commented 5 years ago

Thank you. Everything is installed and I'm running through the demo. Thanks so much for the quick response 👍