Error in installation: BSgenome.Hsapiens.UCSC.hg38 not available

[ccnawrocki]

Hello, when I try to install the package, I am getting the following error message. I would appreciate any help you could possibly offer me.

> devtools::install_github("satijalab/azimuth", "seurat5")
Downloading GitHub repo satijalab/azimuth@seurat5
Installing 1 packages: BSgenome.Hsapiens.UCSC.hg38
Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'installing the source package ‘BSgenome.Hsapiens.UCSC.hg38’

trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz'
Content type 'application/x-gzip' length 731245539 bytes (697.4 MB)
=========
downloaded 137.7 MB

Warning: downloaded length 0 != reported length 0Warning: URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz': Timeout of 60 seconds was reachedError in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz' failed
Warning: download of package ‘BSgenome.Hsapiens.UCSC.hg38’ failed── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/_6/qhytbgh10k5cp65dy9zhhcym0000gp/T/RtmpBWXqoE/remotes7b0e39641261/satijalab-azimuth-f50f441/DESCRIPTION’ ...
─  preparing ‘Azimuth’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Omitted ‘LazyData’ from DESCRIPTION
─  building ‘Azimuth_0.4.6.9004.tar.gz’

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: installation of package ‘/var/folders/_6/qhytbgh10k5cp65dy9zhhcym0000gp/T//RtmpBWXqoE/file7b0e23aa931b/Azimuth_0.4.6.9004.tar.gz’ had non-zero exit status
> 

[Gesmira]

Hi, Have you tried installing BSGenome before running the Azimuth install? https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html

[ccnawrocki]

Hi, Your suggestion helped with the installation. Once I did,

BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
library(BSgenome.Hsapiens.UCSC.hg38)
install.packages("Signac")
library(Signac)

Then, installing Azimuth was fine.

But, now I am having another problem:

> LUNG4 <- RunAzimuth(query = LUNG2,reference = "lungref")
Warning: Overwriting miscellanous data for modelWarning: Adding a dimensional reduction (refUMAP) without the associated assay being presentdetected inputs from HUMAN with id type Gene.name
reference rownames detected HUMAN with id type Gene.name
Normalizing query using reference SCT model
Warning: 2483 features of the features specified were not present in both the reference query assays. 
Continuing with remaining 517 features.Projecting cell embeddings
Finding query neighbors
Finding neighborhoods
Finding anchors
    Found 9092 anchors
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Predicting cell labels
Error in possible.ids[apply(X = prediction.scores, MARGIN = 1, FUN = which.max)] : 
  invalid subscript type 'list'

How do I fix this?

[ccnawrocki]

I am going to close this issue, as I ended up getting it to work. I think it was just a syntax-esque error on my end.