##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:xCell2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings xCell2_0.99.109.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/xCell2.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xCell2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘xCell2’ version ‘0.99.109’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘xCell2’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    help   2.9Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dice_demo_ref.Rd: SummarizedExperiment-class
  xCell2Analysis.Rd: BiocParallelParam-class
  xCell2GetLineage.Rd: AnnotationHub, ontologyIndex
  xCell2Train.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, BiocParallelParam-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test-xCell2Train.R:91:3
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─xCell2::xCell2Train(...)
   7.   └─xCell2:::ValidateInputs(ref, labels, refType)
   8.     ├─labels[, c("ont", "label", "sample", "dataset")]
   9.     └─base::`[.data.frame`(labels, , c("ont", "label", "sample", "dataset"))
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 41 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/xCell2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL xCell2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘xCell2’ ...
** this is package ‘xCell2’ version ‘0.99.109’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (xCell2)

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(xCell2)
> 
> test_check("xCell2")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 41 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-xCell2Train.R:91:3'): xCell2Train validates inputs correctly ──
`xCell2Train(ref = dice_ref, labels = insufficient_labels, refType = "rnaseq")` threw an error with unexpected message.
Expected match: "Reference must have at least 3 cell types!"
Actual message: "undefined columns selected"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test-xCell2Train.R:91:3
 2. │ └─testthat:::quasi_capture(...)
 3. │   ├─testthat (local) .capture(...)
 4. │   │ └─base::withCallingHandlers(...)
 5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 6. └─xCell2::xCell2Train(...)
 7.   └─xCell2:::ValidateInputs(ref, labels, refType)
 8.     ├─labels[, c("ont", "label", "sample", "dataset")]
 9.     └─base::`[.data.frame`(labels, , c("ont", "label", "sample", "dataset"))

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 41 ]
Error: Test failures
Execution halted