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CHECK report for coexnet on tokay1

This page was generated on 2019-04-13 11:27:57 -0400 (Sat, 13 Apr 2019).

Package 303/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coexnet 1.4.0
Juan David Henao
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/coexnet
Branch: RELEASE_3_8
Last Commit: 053d9b7
Last Changed Date: 2018-10-30 11:42:05 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: coexnet
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coexnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings coexnet_1.4.0.tar.gz
StartedAt: 2019-04-13 01:23:39 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:28:37 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 298.2 seconds
RetCode: 0
Status:  OK  
CheckDir: coexnet.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coexnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings coexnet_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/coexnet.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
findThreshold 7.47      1    8.46
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
findThreshold 6.39   0.69    7.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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: OK


Installation output

coexnet.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/coexnet_1.4.0.tar.gz && rm -rf coexnet.buildbin-libdir && mkdir coexnet.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=coexnet.buildbin-libdir coexnet_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL coexnet_1.4.0.zip && rm coexnet_1.4.0.tar.gz coexnet_1.4.0.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
100 1748k  100 1748k    0     0  28.9M      0 --:--:-- --:--:-- --:--:-- 31.0M

install for i386

* installing *source* package 'coexnet' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'coexnet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coexnet' as coexnet_1.4.0.zip
* DONE (coexnet)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'coexnet' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

coexnet.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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)
Achieved FDR: 0.0975Achieved FDR: 0.0478571428571429Warning: 4 parsing failures.
row col   expected     actual         file
118  -- 16 columns 15 columns literal data
119  -- 16 columns 13 columns literal data
121  -- 16 columns 15 columns literal data
122  -- 16 columns 15 columns literal data



RUNIT TEST PROTOCOL -- Sat Apr 13 01:28:20 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
coexnet RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  13.31    0.76   14.10 

coexnet.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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: 0.0975Achieved FDR: 0.0478571428571429Warning: 4 parsing failures.
row col   expected     actual         file
118  -- 16 columns 15 columns literal data
119  -- 16 columns 13 columns literal data
121  -- 16 columns 15 columns literal data
122  -- 16 columns 15 columns literal data



RUNIT TEST PROTOCOL -- Sat Apr 13 01:28:33 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
coexnet RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  13.01    0.39   13.39 

Example timings

coexnet.Rcheck/examples_i386/coexnet-Ex.timings

nameusersystemelapsed
CCP0.030.000.03
cofVar0.050.020.06
createNet1.790.011.91
difExprs0.630.000.63
exprMat000
findThreshold7.471.008.46
geneSymbol0.040.020.19
getAffy0.660.000.83
getInfo000
ppiNet0.020.000.02
sharedComponents0.010.000.01

coexnet.Rcheck/examples_x64/coexnet-Ex.timings

nameusersystemelapsed
CCP0.050.000.04
cofVar0.250.000.25
createNet1.510.001.53
difExprs0.410.040.45
exprMat000
findThreshold6.390.697.08
geneSymbol0.010.020.03
getAffy0.830.010.85
getInfo000
ppiNet000
sharedComponents0.020.000.02