##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SpatialDecon_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialDecon.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialDecon/DESCRIPTION’ ... OK
* this is package ‘SpatialDecon’ version ‘1.14.0’
* 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 ‘SpatialDecon’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
download_profile_matrix: no visible binding for global variable
  ‘profile_matrix’
Undefined global functions or variables:
  profile_matrix
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
runCollapseCellTypes 131.173  0.667 132.101
runReverseDecon      130.392  0.199 130.830
runspatialdecon       65.496  1.026  67.948
runMergeTumorIntoX    22.454  0.132  22.635
runErrorModel         21.619  0.124  21.791
reverseDecon          10.108  0.319  10.450
SpatialDecon-package   5.189  0.036   5.235
* 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:
  [1] "2 / 4 : C"
  [1] "3 / 4 : A"
  [1] "4 / 4 : D"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-integration-testing.R:105:3'): spatialdeconTILs is as expected: beta ──
  all(abs(res.test$beta - res$beta) < 0.01) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialDecon.Rcheck/00check.log’
for details.