BiocManager::install("MangiolaLaboratory/HPCell")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.21 (BiocManager 1.30.26), R 4.5.1 (2025-06-13)
Installing github package(s) 'MangiolaLaboratory/HPCell'
Downloading GitHub repo MangiolaLaboratory/HPCell@HEAD
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: ragg (1.4.0 -> 1.5.0) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 3
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpbwJo6s/remotes14ae8a738d70f7/MangiolaLaboratory-HPCell-3d78886/DESCRIPTION’ (1.7s)
─ preparing ‘HPCell’: (846ms)
✔ checking DESCRIPTION meta-information ... OK
─ checking for LF line-endings in source and make files and shell scripts (1.2s)
─ checking for empty or unneeded directories
Removed empty directory ‘HPCell/.github/ISSUE_TEMPLATE’
NB: this package now depends on R (>= 4.3.0)
WARNING: Added dependency on R >= 4.3.0 because package code uses the
pipe placeholder at the head of a chain of extractions syntax added
in R 4.3.0.
File(s) using such syntax:
‘functions.R’ ‘utilities.R’
─ building ‘HPCell_0.3.13.tar.gz’
* installing *source* package ‘HPCell’ ...
** this is package ‘HPCell’ version ‘0.3.13’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘broom::tidy’ by ‘tidySingleCellExperiment::tidy’ when loading ‘HPCell’
Warning: replacing previous import ‘tidySingleCellExperiment::tidy’ by ‘tidySummarizedExperiment::tidy’ when loading ‘HPCell’
Warning: replacing previous import ‘tidySummarizedExperiment::tidy’ by ‘tidyseurat::tidy’ when loading ‘HPCell’
Warning: replacing previous import ‘tidySingleCellExperiment::join_transcripts’ by ‘tidyseurat::join_transcripts’ when loading ‘HPCell’
Warning: replacing previous import 'magrittr::set_names' by 'purrr::set_names' when loading 'HPCell'
in method for 'test_differential_abundance' with signature '.data="HPCell"': no definition for class "HPCell"
Error : in method for 'test_differential_abundance' with signature '.data="HPCell"': formal arguments in method and generic do not appear in the same order
Error: unable to load R code in package 'HPCell'
Execution halted
ERROR: lazy loading failed for package ‘HPCell’
* removing ‘/home/users/allstaff/mangiola.s/R/x86_64-pc-linux-gnu-library/4.5/HPCell’
Installation paths not writeable, unable to update packages
path: /stornext/System/data/software/rhel/9/base/tools/R/4.5.1/lib64/R/library
packages:
boot, here, Matrix
Old packages: 'arrow', 'bayesplot', 'brms', 'checkmate', 'ComplexHeatmap', 'credentials', 'dendextend', 'dtplyr', 'duckdb', 'gargle',
'glmmTMB', 'googledrive', 'googlesheets4', 'GSEABase', 'haven', 'InteractionSet', 'priorsense', 'quarto', 'ragg', 'renv',
'roxygen2', 'rstantools', 'rvest', 'Seurat', 'singscore', 'svUnit', 'tidyHeatmap', 'usethis', 'waldo'
Update all/some/none? [a/s/n]:
n
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpbwJo6s/file14ae8a66067df/HPCell_0.3.13.tar.gz’ had non-zero exit status
