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This page was generated on 2021-12-06 13:05:53 -0500 (Mon, 06 Dec 2021).

CHECK results for coexnet on machv2

To the developers/maintainers of the coexnet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/coexnet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 367/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coexnet 1.16.0  (landing page)
Juan David Henao
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/coexnet
git_branch: RELEASE_3_14
git_last_commit: 8ddee4f
git_last_commit_date: 2021-10-26 12:35:58 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: coexnet
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coexnet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coexnet_1.16.0.tar.gz
StartedAt: 2021-12-05 13:10:01 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 13:14:27 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 265.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: coexnet.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coexnet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coexnet_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/coexnet.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coexnet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coexnet’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
findThreshold 12.088  0.875  12.972
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/coexnet.Rcheck/00check.log’
for details.


Installation output

coexnet.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL coexnet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
** 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)

Tests output

coexnet.Rcheck/tests/runTests.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 0.198 0.02 0.219
Error in checkEqualsNumeric(findThreshold(expData = data[1:5, ], method = "correlation"),  : 
  'is.NA' value mismatch: 0 in current 1 in target

Timing stopped at: 0.019 0.003 0.023
Error in checkEquals(final_table$ID[1], "Os03g0669200") : 
  'is.NA' value mismatch: 0 in current 1 in target



RUNIT TEST PROTOCOL -- Sun Dec  5 13:14:15 2021 
*********************************************** 
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

Example timings

coexnet.Rcheck/coexnet-Ex.timings

nameusersystemelapsed
CCP0.0220.0030.025
cofVar0.0540.0060.059
createNet1.8320.0251.858
difExprs1.0950.0581.154
exprMat0.0000.0010.001
findThreshold12.088 0.87512.972
geneSymbol0.0170.0040.023
getAffy0.4530.0090.464
getInfo0.0000.0010.000
ppiNet0.0060.0010.006
sharedComponents0.0060.0030.010