Is there anyone who downloaded Azimuth packges?

Question

[kayah]

I want to annotation my clusters by Azimuth package.... I tried to install 'Azimuth' packages several code but it didn't work. If you know, please teach how to install Azimuth. Or If you know another tip to annotation please tell me. Thank you so much!! fist tried code is

 devtools::install_github("satijalab/azimuth", "seurat5")
    devtools::install_github("satijalab/azimuth")

second tried code is

if (!requireNamespace('remotes', quietly = TRUE) {
  install.packages('remotes')
}
remotes::install_github('satijalab/azimuth', ref = 'master')

[fracarb8]

It is difficult to help without seeing the error messages. Also set quietly=FALSE to see what is happening in the console.

[kayah]

Error in download.file(url, destfile, method, mode = "wb", ...) : 
   download from 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz' failed
    ERROR: dependency ‘BSgenome.Hsapiens.UCSC.hg38’ is not available for package ‘Azimuth’
    * removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Azimuth’
    Warning messages:
    1: In i.p(...) : installation of package ‘igraph’ had non-zero exit status
    2: In i.p(...) :
      installation of package ‘/var/folders/sy/rt64kdpd5v172_6w54jnz_bh0000gn/T//RtmpM05ry5/fileaf997b03db36/Azimuth_0.5.0.tar.gz’ had non-zero exit status

[fracarb8]

ERROR: dependency ‘BSgenome.Hsapiens.UCSC.hg38’ is not available for package ‘Azimuth’. did you installed it? Also check if igraph can be laoded.

[kayah]

Then I should download all annotation files before install 'Azimuth'? Thanks for help!

[fracarb8]

Yes, you need to have installed all packages azimuth depends on.

Answer 1

[Hatchet]

igraph can't be loaded it's visible from the fact that azimuth needed igraph, so it automatically tried to install it but failed, and because it failed azimuth did not install either. Run the install command for igraph it will fail but it will tell you what are the dependencies for it. And also try to install it's dependencies one by one. Rinse and repeat. There will be dependencies that you have to install from the command line and not rStudio. Most likely it will be tedious.

Answer 2

[pariapooyan]

Yes, I finally did :-D

install.packages("BiocManager")

library(BiocManager)

# DirichletMultinomial #
if (!require("BiocManager", quietly = TRUE))

 install.packages("BiocManager")

BiocManager::install("DirichletMultinomial", force = TRUE)

library(DirichletMultinomial)

# TFBSTools #
if (!require("BiocManager", quietly = TRUE))

  install.packages("BiocManager")

BiocManager::install("TFBSTools")

library(TFBSTools)

# BSgenome.Hsapiens.UCSC.hg38 #
if (!require("BiocManager", quietly = TRUE))

  install.packages("BiocManager")

options(timeout=10000)

BiocManager::install("BSgenome.Hsapiens.UCSC.hg38", force = TRUE)

library(BSgenome.Hsapiens.UCSC.hg38) # Error in library(BSgenome.Hsapiens.UCSC.hg38) : there is no package called ‘BSgenome.Hsapiens.UCSC.hg38’  a


BiocManager::valid()

BiocManager::install(version = "3.20")

options(timeout = 3000) # I also used ethernet connection

BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

library(BSgenome.Hsapiens.UCSC.hg38)

.rs.restartR()

library(BiocManager)

library(DirichletMultinomial)

library(TFBSTools)

library(BSgenome.Hsapiens.UCSC.hg38)

library(usethis)

library(devtools)

devtools::install_github("satijalab/azimuth", "seurat5")

[ATpoint]

Or just BiocManager::install("satijalab/azimuth") since this will install from GitHub and take care of CRAN and Bioc dependencies. Wouldn't that do?

[pariapooyan]

This one had not worked for me as well.

[ATpoint]

I just tried and it worked beautifully. If you have issues then try to find the root, such uncustom and manual installation with forced restarts etc is laborious.