Multiple platform build/check report for BioC 3.14 - CHECK results for coexnet on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: coexnet

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coexnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings coexnet_1.16.0.tar.gz

StartedAt: 2022-04-12 17:40:33 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:45:19 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 286.5 seconds

RetCode: 1

Status: ERROR

CheckDir: coexnet.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coexnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings coexnet_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/coexnet.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.16.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
findThreshold 9.33   0.58    9.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
findThreshold 14.36   0.43   14.78
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  FAILURE in test_ppiNet: Error in checkEqualsNumeric(length(ppi), 10) : 
    Mean relative difference: 0.6666667
  
  
  Test files with failing tests
  
     test_coexnet.R 
       test_CCP 
       test_geneSymbol 
       test_ppiNet 
  
  
  Error in BiocGenerics:::testPackage("coexnet") : 
    unit tests failed for package coexnet
  Execution halted
** running tests for arch 'x64' ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  FAILURE in test_ppiNet: Error in checkEqualsNumeric(length(ppi), 10) : 
    Mean relative difference: 0.6666667
  
  
  Test files with failing tests
  
     test_coexnet.R 
       test_CCP 
       test_geneSymbol 
       test_ppiNet 
  
  
  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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/coexnet.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/coexnet_1.16.0.tar.gz && rm -rf coexnet.buildbin-libdir && mkdir coexnet.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=coexnet.buildbin-libdir coexnet_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL coexnet_1.16.0.zip && rm coexnet_1.16.0.tar.gz coexnet_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 47 1742k   47  821k    0     0  1288k      0  0:00:01 --:--:--  0:00:01 1289k
100 1742k  100 1742k    0     0  1609k      0  0:00:01  0:00:01 --:--:-- 1610k

install for i386

* 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

install for x64

* installing *source* package 'coexnet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coexnet' as coexnet_1.16.0.zip
* DONE (coexnet)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'coexnet' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)
Timing stopped at: 0.02 0 0.01
Error in checkEqualsNumeric(length(ccp), 10) : 
  Mean relative difference: 1

Achieved FDR: 0.0979166666666667Achieved FDR: 0.0463636363636364Timing stopped at: 0.03 0 0.05
Error in checkEquals(final_table$ID[1], "Os03g0669200") : 
  'is.NA' value mismatch: 0 in current 1 in target

Timing stopped at: 0.01 0 0.02
Error in checkEqualsNumeric(length(ppi), 10) : 
  Mean relative difference: 0.6666667



RUNIT TEST PROTOCOL -- Tue Apr 12 17:44:58 2022 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 3 

 
1 Test Suite : 
coexnet RUnit Tests - 10 test functions, 0 errors, 3 failures
FAILURE in test_CCP: Error in checkEqualsNumeric(length(ccp), 10) : 
  Mean relative difference: 1

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

FAILURE in test_ppiNet: Error in checkEqualsNumeric(length(ppi), 10) : 
  Mean relative difference: 0.6666667


Test files with failing tests

   test_coexnet.R 
     test_CCP 
     test_geneSymbol 
     test_ppiNet 


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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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)
Timing stopped at: 0.01 0 0.01
Error in checkEqualsNumeric(length(ccp), 10) : 
  Mean relative difference: 1

Achieved FDR: 0.0979166666666667Achieved FDR: 0.0463636363636364Timing stopped at: 0 0 0.04
Error in checkEquals(final_table$ID[1], "Os03g0669200") : 
  'is.NA' value mismatch: 0 in current 1 in target

Timing stopped at: 0 0 0
Error in checkEqualsNumeric(length(ppi), 10) : 
  Mean relative difference: 0.6666667



RUNIT TEST PROTOCOL -- Tue Apr 12 17:45:11 2022 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 3 

 
1 Test Suite : 
coexnet RUnit Tests - 10 test functions, 0 errors, 3 failures
FAILURE in test_CCP: Error in checkEqualsNumeric(length(ccp), 10) : 
  Mean relative difference: 1

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

FAILURE in test_ppiNet: Error in checkEqualsNumeric(length(ppi), 10) : 
  Mean relative difference: 0.6666667


Test files with failing tests

   test_coexnet.R 
     test_CCP 
     test_geneSymbol 
     test_ppiNet 


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

name	user	system	elapsed
CCP	0.02	0.02	0.03
cofVar	0.05	0.01	0.06
createNet	1.15	0.00	1.78
difExprs	0.75	0.05	0.80
exprMat	0	0	0
findThreshold	9.33	0.58	9.91
geneSymbol	0.05	0.00	0.83
getAffy	1.22	0.04	1.45
getInfo	0	0	0
ppiNet	0	0	0
sharedComponents	0.00	0.02	0.01

name	user	system	elapsed
CCP	0.03	0.00	0.03
cofVar	0.01	0.00	0.02
createNet	1.72	0.04	2.24
difExprs	0.72	0.00	0.72
exprMat	0	0	0
findThreshold	14.36	0.43	14.78
geneSymbol	0.03	0.00	0.76
getAffy	0.61	0.01	0.63
getInfo	0	0	0
ppiNet	0.01	0.00	0.02
sharedComponents	0.02	0.00	0.01

CHECK results for coexnet on tokay2

Summary

Command output

Installation output

Tests output

Example timings