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CHECK report for CHRONOS on tokay1

This page was generated on 2019-04-13 11:26:42 -0400 (Sat, 13 Apr 2019).

Package 262/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CHRONOS 1.10.1
Panos Balomenos
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/CHRONOS
Branch: RELEASE_3_8
Last Commit: 84084b5
Last Changed Date: 2019-03-28 20:36:02 -0400 (Thu, 28 Mar 2019)
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: CHRONOS
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CHRONOS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CHRONOS_1.10.1.tar.gz
StartedAt: 2019-04-13 01:13:33 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:17:21 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 228.6 seconds
RetCode: 0
Status:  OK  
CheckDir: CHRONOS.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:CHRONOS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CHRONOS_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/CHRONOS.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 'CHRONOS/DESCRIPTION' ... OK
* this is package 'CHRONOS' version '1.10.1'
* 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 'CHRONOS' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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

CHRONOS.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/CHRONOS_1.10.1.tar.gz && rm -rf CHRONOS.buildbin-libdir && mkdir CHRONOS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CHRONOS.buildbin-libdir CHRONOS_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CHRONOS_1.10.1.zip && rm CHRONOS_1.10.1.tar.gz CHRONOS_1.10.1.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
 41  932k   41  384k    0     0  3547k      0 --:--:-- --:--:-- --:--:-- 3622k
100  932k  100  932k    0     0  7567k      0 --:--:-- --:--:-- --:--:-- 7705k

install for i386

* installing *source* package 'CHRONOS' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CHRONOS'
    finding HTML links ... done
    CHRONOSrun                              html  
    convertMiRNANomenclature                html  
    convertNomenclature                     html  
    createPathwayGraphs                     html  
    downloadKEGGPathwayList                 html  
    downloadMiRecords                       html  
    downloadPathways                        html  
    extractLinearSubpathways                html  
    extractNonLinearSubpathways             html  
    getEdgeTypes                            html  
    importExpressions                       html  
    pathwayMeasures                         html  
    scoreSubpathways                        html  
    subpathwayKEGGmap                       html  
    subpathwayMiRNAs                        html  
    visualizeResults                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CHRONOS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CHRONOS' as CHRONOS_1.10.1.zip
* DONE (CHRONOS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CHRONOS' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

CHRONOS.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('CHRONOS')
Testing test_CHRONOSrun...Importing entrezgene data...done.
Importing miRNA data...done.
Downloading files...done.
Creating adjacency matrices...done.
Extracting Linear Subpathways...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
Extracting Non Linear Subpathways...done.
	#24 subpathways initially
Calculating subscores...done.
	#19 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_pathwayToGraph...Creating adjacency matrices...done.
done.
Testing test_subExtractionLinear...Importing entrezgene data...done.
Extracting Linear Subpathways...done.
done.
Testing test_subExtractionNonLinear...Importing entrezgene data...done.
Extracting Non Linear Subpathways...done.
done.
Testing test_subRefinement...Importing entrezgene data...done.
Importing miRNA data...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_subVisualization...Importing entrezgene data...done.
Summarising scores...Note: zip::zip() is deprecated, please use zip::zipr() instead
done.
Summarising scores...done.
done.


RUNIT TEST PROTOCOL -- Sat Apr 13 01:17:00 2019 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CHRONOS RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
   8.75    0.71   16.95 

CHRONOS.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('CHRONOS')
Testing test_CHRONOSrun...Importing entrezgene data...done.
Importing miRNA data...done.
Downloading files...done.
Creating adjacency matrices...done.
Extracting Linear Subpathways...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
Extracting Non Linear Subpathways...done.
	#24 subpathways initially
Calculating subscores...done.
	#19 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_pathwayToGraph...Creating adjacency matrices...done.
done.
Testing test_subExtractionLinear...Importing entrezgene data...done.
Extracting Linear Subpathways...done.
done.
Testing test_subExtractionNonLinear...Importing entrezgene data...done.
Extracting Non Linear Subpathways...done.
done.
Testing test_subRefinement...Importing entrezgene data...done.
Importing miRNA data...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_subVisualization...Importing entrezgene data...done.
Summarising scores...Note: zip::zip() is deprecated, please use zip::zipr() instead
done.
Summarising scores...done.
done.


RUNIT TEST PROTOCOL -- Sat Apr 13 01:17:16 2019 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CHRONOS RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
   8.14    0.73   16.50 

Example timings

CHRONOS.Rcheck/examples_i386/CHRONOS-Ex.timings

nameusersystemelapsed
CHRONOSrun1.000.122.94
convertMiRNANomenclature0.000.020.02
convertNomenclature000
createPathwayGraphs0.30.00.3
downloadKEGGPathwayList0.030.000.03
downloadMiRecords0.050.000.05
downloadPathways000
extractLinearSubpathways0.280.091.87
extractNonLinearSubpathways0.310.030.35
getEdgeTypes000
importExpressions0.070.000.06
pathwayMeasures0.120.000.12
scoreSubpathways0.110.000.11
subpathwayKEGGmap0.030.020.05
subpathwayMiRNAs0.740.000.89
visualizeResults0.310.032.45

CHRONOS.Rcheck/examples_x64/CHRONOS-Ex.timings

nameusersystemelapsed
CHRONOSrun1.050.052.44
convertMiRNANomenclature0.010.000.01
convertNomenclature000
createPathwayGraphs0.350.010.36
downloadKEGGPathwayList0.030.000.03
downloadMiRecords0.030.000.03
downloadPathways000
extractLinearSubpathways0.420.102.17
extractNonLinearSubpathways0.300.030.33
getEdgeTypes000
importExpressions0.060.000.07
pathwayMeasures0.130.000.12
scoreSubpathways0.120.000.13
subpathwayKEGGmap0.030.000.03
subpathwayMiRNAs0.850.000.84
visualizeResults0.070.012.14