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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sparrow.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sparrow_1.11.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sparrow/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sparrow' version '1.11.0'
* 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 whether package 'sparrow' 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 whether startup messages can be suppressed ... 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
geneSetsStats: no visible binding for global variable 'direction'
Undefined global functions or variables:
  direction
* checking Rd files ... NOTE
checkRd: (-1) convertIdentifiers.Rd:118: Lost braces; missing escapes or markup?
   118 | rely on the {babelgene} package for the conversion, so you will have to
       |             ^
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
goseq              8.61  16.48   25.17
scoreSingleSamples 4.60   2.13    5.38
seas               6.18   0.23    6.33
* 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:
  GSVA::plage
  ── Failure ('test-scoreSingleSamples.R:27:5'): do.scoreSingleSamples.gsva produces correct gsva,plage,ssGSEA scores ──
  `res` not equal to `ex`.
  Attributes: < Component "geneSets": Component "c2;;HUPER_BREAST_BASAL_VS_LUMINAL_UP": 33 string mismatches >
  Attributes: < Component "geneSets": Component "c6;;CYCLIN_D1_UP.V1_DN": 108 string mismatches >
  Attributes: < Component "geneSets": Component "c6;;KRAS.600.LUNG.BREAST_UP.V1_UP": 146 string mismatches >
  Attributes: < Component "geneSets": Component "c6;;KRAS.BREAST_UP.V1_UP": 56 string mismatches >
  Attributes: < Component "geneSets": Component "c6;;KRAS.LUNG.BREAST_UP.V1_UP": 73 string mismatches >
  Attributes: < Component "geneSets": Component "c7;;GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN": 59 string mismatches >
  Attributes: < Component "geneSets": Component "c7;;GSE3982_BCELL_VS_TH2_DN": 50 string mismatches >
  GSVA::ssgsea
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 1484 ]
  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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck/00check.log'
for details.