##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:geva.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings geva_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/geva.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘geva/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geva’ version ‘1.10.0’
* 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 ‘geva’ 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 R 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
geva.quick    37.666  0.220  37.887
geva.finalize 18.116  0.004  18.120
top.genes     16.818  0.004  16.822
geva.cluster   5.441  0.332   5.773
geva.hcluster  5.687  0.000   5.688
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘geva.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘geva.Rmd’
  ...
+         lev = 0
+     devtools::load_all(getwd())
+ }

  When sourcing ‘geva.R’:
Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in
'/tmp/Rtmpbk1U1t/file2d9dd97d42e7df/vignettes'.
ℹ Are you in your project directory and does your project have a 'DESCRIPTION'
  file?
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/geva.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL geva
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘geva’ ...
** using staged installation
** R
** 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 (geva)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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(geva)
> 
> test_check("geva")
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 54 significant genes:
similar: 33
factor-specific: 7
factor-dependent: 14
Input summarized
Calculating hierarchical clustering...
Found 6 clusters
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 60 significant genes:
factor-specific: 18
factor-dependent: 39
similar: 3
Testing plot with GEVAResults
Testing with cluster.method = 'hierarchical'
Calculating hierarchical clustering...
Found 6 clusters
Testing with cluster.method = 'density'
Calculating density clustering...
Found 3 clusters
Testing quantiles grouping
Testing with quantile.method = 'range.slice'
Testing with quantile.method = 'proportional'
Testing with quantile.method = 'density'
Testing with quantile.method = 'k.max.sd'
Testing with quantile.method = 'custom'
Testing plot with GEVACluster and GEVAQuantiles
Reading 'gevainput2d8e8e1781a4b5.txt' ...
Reading 'gevainput2d8e8e24be5de8.txt' ...
Reading 'gevainput2d8e8e3d50f7fd.txt' ...
Reading 'gevainput2d8e8e6cb1556c.txt' ...
Reading 'gevainput2d8e8e6276d394.txt' ...
Reading 'gevainput2d8e8e38ab2731.txt' ...
Reading 'gevainput2d8e8e6127f055.txt' ...
Reading 'gevainput2d8e8e729c3a04.txt' ...
Reading 'gevainput2d8e8e1faf34d6.txt' ...
Read 9 columns with 10000 probes
Testing with summary.method = 'mean'
Testing with summary.method = 'median'
Testing with variation.method = 'sd'
Testing with variation.method = 'var'
Testing with variation.method = 'mad'
Testing plot with GEVASummary
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 43.764   0.545  44.298