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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:fgga.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings fgga_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/fgga.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘fgga/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fgga’ version ‘1.9.0’
* 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 ‘fgga’ 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 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
svmOnto  17.432  0.116  17.549
svmTrain 16.412  0.087  16.500
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  fgga RUnit Tests - 11 test functions, 0 errors, 1 failure
  FAILURE in test_svm: Error in checkEquals(mT[1, 6], 0.9999) : 
    Mean relative difference: 313.5138
  
  
  Test files with failing tests
  
     test_svm.R 
       test_svm 
  
  
  Error in BiocGenerics:::testPackage("fgga") : 
    unit tests failed for package fgga
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘fgga.Rmd’ using ‘UTF-8’... OK
 NONE
* 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/fgga.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL fgga
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘fgga’ ...
** 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 (fgga)

R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> BiocGenerics:::testPackage("fgga")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Term: GO:0000166
Term: GO:0003674
Term: GO:0003676
Term: GO:0003677
Term: GO:0003824
Term: GO:0004888
Term: GO:0005102
Term: GO:1901363
Term: GO:1902494
Term: GO:1990234
Term: Ontology:FES
Term:GO:0000166
Term:GO:0003674
Term:GO:0003676
Term:GO:0003677
Term:GO:0003824
Term:GO:0004888
Term:GO:0005102
Term:GO:1901363
Term:GO:1902494
Term:GO:1990234
Term:Ontology:FES
Term: GO:0001
Term: GO:0002
Term: GO:0003
Term: GO:0004
Term: GO:0005
Term: Ontology:FES
Term: GO:0007
Term: GO:0008
Term: GO:0009
Timing stopped at: 0.112 0.116 0.228
Error in checkEquals(mT[1, 6], 0.9999) : 
  Mean relative difference: 313.5138



RUNIT TEST PROTOCOL -- Tue May 30 07:18:38 2023 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
fgga RUnit Tests - 11 test functions, 0 errors, 1 failure
FAILURE in test_svm: Error in checkEquals(mT[1, 6], 0.9999) : 
  Mean relative difference: 313.5138


Test files with failing tests

   test_svm.R 
     test_svm 


Error in BiocGenerics:::testPackage("fgga") : 
  unit tests failed for package fgga
Execution halted