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BlishLab / scriabin

Analysis of cell-cell communication at single-cell resolution
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Installation error #18

Closed ndrubins closed 8 months ago

ndrubins commented 8 months ago

Hi,

I'm trying to install scriabin (devtools::install_github("BlishLab/scriabin", ref = "main")) but I'm getting this error message:

> devtools::install_github("BlishLab/scriabin", ref = "main")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo BlishLab/scriabin@main
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: DelayedMa... (1.16.0       -> 1.24.0      ) [CRAN]
5: Summarize... (1.24.0       -> 1.32.0      ) [CRAN]
6: reticulate   (38f49a79f... -> 5d0a9a522...) [GitHub]
7: genefilter   (1.76.0       -> 1.84.0      ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpFnUDWB/remotes14799a6fd3a6e3/BlishLab-scriabin-adf1645/DESCRIPTION’ ...
─  preparing ‘scriabin’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
     NB: this package now depends on R (>= 3.5.0)
     WARNING: Added dependency on R >= 3.5.0 because serialized objects in
     serialize/load version 3 cannot be read in older versions of R.
     File(s) containing such objects:
       ‘scriabin/inst/lr_resources.rds’
─  building ‘scriabin_0.0.0.9000.tar.gz’

Installing package into ‘/home/nrubinstein/R’
(as ‘lib’ is unspecified)
* installing *source* package ‘scriabin’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: multiple methods tables found for ‘acbind’
Warning: multiple methods tables found for ‘arbind’
Warning: replacing previous import ‘SingleCellExperiment::counts<-’ by ‘scater::counts<-’ when loading ‘CelliD’
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘scater::cpm’ when loading ‘CelliD’
Warning: replacing previous import ‘SingleCellExperiment::cpm<-’ by ‘scater::cpm<-’ when loading ‘CelliD’
Warning: replacing previous import ‘SingleCellExperiment::counts’ by ‘scater::counts’ when loading ‘CelliD’
Warning: replacing previous import ‘SingleCellExperiment::tpm’ by ‘scater::tpm’ when loading ‘CelliD’
Warning: replacing previous import ‘SingleCellExperiment::tpm<-’ by ‘scater::tpm<-’ when loading ‘CelliD’
Warning: replacing previous import ‘data.table::shift’ by ‘tictoc::shift’ when loading ‘CelliD’
Warning: replacing previous import ‘cowplot::get_legend’ by ‘ggpubr::get_legend’ when loading ‘scriabin’
Error: objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:BiocGenerics'
Execution halted
ERROR: lazy loading failed for package ‘scriabin’
* removing ‘/home/nrubinstein/R/scriabin’

Might there be calls to ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ without the preceding Matrix reference?