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CHECK report for pwOmics on merida2

This page was generated on 2019-04-09 13:31:35 -0400 (Tue, 09 Apr 2019).

Package 1255/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pwOmics 1.15.0
Maren Sitte
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/pwOmics
Branch: master
Last Commit: d8a6046
Last Changed Date: 2018-10-30 11:54:34 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: pwOmics
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pwOmics_1.15.0.tar.gz
StartedAt: 2019-04-09 03:04:30 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:11:32 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 421.5 seconds
RetCode: 0
Status:  OK 
CheckDir: pwOmics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pwOmics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pwOmics_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pwOmics.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pwOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pwOmics’ version ‘1.15.0’
* 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 ‘pwOmics’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
identifyPWTFTGs: no visible binding for global variable ‘upreg’
identifyPWTFTGs: no visible binding for global variable ‘phosphoeffect’
infoConsensusGraph: no visible global function definition for ‘from’
Undefined global functions or variables:
  from phosphoeffect upreg
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
temp_correlations 268.848  3.028 276.895
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/pwOmics.Rcheck/00check.log’
for details.



Installation output

pwOmics.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pwOmics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘pwOmics’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pwOmics)

Tests output

pwOmics.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("pwOmics")


RUNIT TEST PROTOCOL -- Tue Apr  9 03:11:24 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
pwOmics RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  5.958   0.341   6.310 

Example timings

pwOmics.Rcheck/pwOmics-Ex.timings

nameusersystemelapsed
clusterTimeProfiles0.0010.0000.000
consDynamicNet000
findSignalingAxes0.0000.0010.000
generate_DSSignalingBase0.0010.0000.000
getBiopaxModel0.0000.0000.001
getDS_PWs0.0000.0010.001
getDS_TFs0.0000.0000.001
getDS_TGs0.0000.0000.001
getGenesIntersection0.0010.0000.001
getOmicsDataset000
getOmicsTimepoints0.0000.0000.001
getOmicsallGeneIDs0.0000.0000.001
getOmicsallProteinIDs0.0000.0000.001
getProteinIntersection0.0000.0000.001
getTFIntersection0.0000.0000.001
getUS_PWs0.0000.0000.001
getUS_TFs0.0010.0010.000
getUS_regulators000
get_matching_transcripts000
gettpIntersection0.0000.0010.000
identifyPR0.0010.0000.000
identifyPWTFTGs000
identifyPWs000
identifyRsofTFs000
identifyTFs0.0010.0000.000
infoConsensusGraph0.0000.0000.001
plotConsDynNet0.0000.0010.001
plotConsensusGraph0.0000.0000.001
plotConsensusProfiles0.0000.0000.001
plotTimeProfileClusters0.0010.0010.000
readOmics000
readPWdata000
readPhosphodata000
readTFdata0.0000.0010.000
staticConsensusNet000
temp_correlations268.848 3.028276.895