##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:scFeatures.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings scFeatures_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/scFeatures.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scFeatures/DESCRIPTION’ ... OK
* this is package ‘scFeatures’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scFeatures’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
Namespaces in Imports field not imported from:
  'DT' 'Seurat'
  All declared Imports should be used.
Missing or unexported object: 'SingleCellSignalR::cell_signaling'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
helper_CCI: no visible global function definition for 'data'
helper_CCI: no visible binding for global variable 'LRdb'
helper_CCI: no visible global function definition for 'capture.output'
helper_pathway_gsva: no visible global function definition for
  'capture.output'
run_pathway_gsva: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  LRdb capture.output data
Consider adding
  importFrom("utils", "capture.output", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scFeatures-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_CCI
> ### Title: Generate cell cell communication score
> ### Aliases: run_CCI
> 
> ### ** Examples
> 
> 
> utils::data("example_scrnaseq" , package = "scFeatures")
> data <- example_scrnaseq[1:1000, 1:100]
Loading required namespace: SeuratObject
> celltype <- data$celltype
> sample <- data$sample
> data <- as.matrix(data@assays$RNA@data)
> 
> alldata <- scFeatures:::formatData(data = data, celltype = celltype, sample = sample )
> feature_CCI <- run_CCI(alldata, type = "scrna" ,  ncores = 1 )
Warning in data(LRdb, package = "SingleCellSignalR") :
  data set 'LRdb' not found
Error: BiocParallel errors
  1 remote errors, element index: 1
  18 unevaluated and other errors
  first remote error:
Error: 'cell_signaling' is not an exported object from 'namespace:SingleCellSignalR'
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘scFeatures_overview.Rmd’ using rmarkdown

Quitting from scFeatures_overview.Rmd:169-178 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'pheatmap'
---
Backtrace:
     ▆
  1. └─scFeatures::run_association_study_report(scfeatures_result, output_folder)
  2.   ├─rmarkdown::render(...)
  3.   │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  4.   │   └─knitr:::process_file(text, output)
  5.   │     ├─xfun:::handle_error(...)
  6.   │     ├─base::withCallingHandlers(...)
  7.   │     └─knitr:::process_group(group)
  8.   │       └─knitr:::call_block(x)
  9.   │         └─knitr:::block_exec(params)
 10.   │           └─knitr:::eng_r(options)
 11.   │             ├─knitr:::in_input_dir(...)
 12.   │             │ └─knitr:::in_dir(input_dir(), expr)
 13.   │             └─knitr (local) evaluate(...)
 14.   │               └─evaluate::evaluate(...)
 15.   │                 ├─base::withRestarts(...)
 16.   │                 │ └─base (local) withRestartList(expr, restarts)
 17.   │                 │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 18.   │                 │   │ └─base (local) doWithOneRestart(return(expr), restart)
 19.   │                 │   └─base (local) withRestartList(expr, restarts[-nr])
 20.   │                 │     └─base (local) withOneRestart(expr, restarts[[1L]])
 21.   │                 │       └─base (local) doWithOneRestart(return(expr), restart)
 22.   │                 ├─evaluate:::with_handlers(...)
 23.   │                 │ ├─base::eval(call)
 24.   │                 │ │ └─base::eval(call)
 25.   │                 │ └─base::withCallingHandlers(...)
 26.   │                 ├─base::withVisible(eval(expr, envir))
 27.   │                 └─base::eval(expr, envir)
 28.   │                   └─base::eval(expr, envir)
 29.   └─base::library(pheatmap)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scFeatures_overview.Rmd' failed with diagnostics:
there is no package called 'pheatmap'
--- failed re-building ‘scFeatures_overview.Rmd’

SUMMARY: processing the following file failed:
  ‘scFeatures_overview.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/scFeatures.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL scFeatures
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘scFeatures’ ...
** this is package ‘scFeatures’ version ‘1.11.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scFeatures)