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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GeoTcgaData.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeoTcgaData_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeoTcgaData.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeoTcgaData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeoTcgaData’ version ‘2.10.0’
* 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 ‘GeoTcgaData’ 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 ... 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
differential_methy 14.892  0.458  15.393
countToFpkm         5.140  0.140   5.292
* 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:
  • On CRAN (2): 'test_diff_RNA_ucsc.R:2:5', 'test_differential_RNA.R:2:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_differential_limma.R:7:5'): can parse example Diff_limma ───────
  Error in ``contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])`: contrasts can be applied only to factors with 2 or more levels
  Backtrace:
      ▆
   1. └─GeoTcgaData::differential_limma(df = df, group = group) at test_differential_limma.R:7:5
   2.   ├─stats::model.matrix(~0 + factor(group))
   3.   └─stats::model.matrix.default(~0 + factor(group))
   4.     └─stats::`contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 10 ]
  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
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GeoTcgaData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GeoTcgaData
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘GeoTcgaData’ ...
** this is package ‘GeoTcgaData’ version ‘2.10.0’
** 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 (GeoTcgaData)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(GeoTcgaData)
> 
> test_check("GeoTcgaData")
file1 is over
file2 is over
file3 is over
file4 is over


'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 10 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_diff_RNA_ucsc.R:2:5', 'test_differential_RNA.R:2:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_differential_limma.R:7:5'): can parse example Diff_limma ───────
Error in ``contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])`: contrasts can be applied only to factors with 2 or more levels
Backtrace:
    ▆
 1. └─GeoTcgaData::differential_limma(df = df, group = group) at test_differential_limma.R:7:5
 2.   ├─stats::model.matrix(~0 + factor(group))
 3.   └─stats::model.matrix.default(~0 + factor(group))
 4.     └─stats::`contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])

[ FAIL 1 | WARN 0 | SKIP 2 | PASS 10 ]
Error: Test failures
Execution halted