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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:coexnet.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings coexnet_1.17.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/coexnet.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'coexnet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coexnet' version '1.17.0'
* 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 'coexnet' 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 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 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
findThreshold 7.25   1.12    8.38
* 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:
  
  FAILURE in test_geneSymbol: Error in checkEquals(final_table$ID[1], "Os03g0669200") : 
    'is.NA' value mismatch: 0 in current 1 in target
  
  
  Test files with failing tests
  
     test_coexnet.R 
       test_findThreshold 
       test_geneSymbol 
  
  
  Error in BiocGenerics:::testPackage("coexnet") : 
    unit tests failed for package coexnet
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'D:/biocbuild/bbs-3.15-bioc/meat/coexnet.Rcheck/00check.log'
for details.

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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL coexnet
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'coexnet' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'coexnet'
    finding HTML links ... done
    CCP                                     html  
    affy                                    html  
    cofVar                                  html  
    createNet                               html  
    difExprs                                html  
    exprMat                                 html  
    findThreshold                           html  
    geneSymbol                              html  
    getAffy                                 html  
    getInfo                                 html  
    info                                    html  
    net1                                    html  
    net2                                    html  
    ppiNet                                  html  
    sharedComponents                        html  
** 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 (coexnet)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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("coexnet")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Achieved FDR: 0.0979166666666667Achieved FDR: 0.0463636363636364Timing stopped at: 0.13 0.03 0.16
Error in checkEqualsNumeric(findThreshold(expData = data[1:5, ], method = "correlation"),  : 
  'is.NA' value mismatch: 0 in current 1 in target

Timing stopped at: 0 0.02 0.01
Error in checkEquals(final_table$ID[1], "Os03g0669200") : 
  'is.NA' value mismatch: 0 in current 1 in target



RUNIT TEST PROTOCOL -- Thu Mar 17 18:49:01 2022 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 2 

 
1 Test Suite : 
coexnet RUnit Tests - 10 test functions, 0 errors, 2 failures
FAILURE in test_findThreshold: Error in checkEqualsNumeric(findThreshold(expData = data[1:5, ], method = "correlation"),  : 
  'is.NA' value mismatch: 0 in current 1 in target

FAILURE in test_geneSymbol: Error in checkEquals(final_table$ID[1], "Os03g0669200") : 
  'is.NA' value mismatch: 0 in current 1 in target


Test files with failing tests

   test_coexnet.R 
     test_findThreshold 
     test_geneSymbol 


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