Package: pwOmics

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2018-10-16 23:25:34 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:32:00 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 385.5 seconds

RetCode: 0

Status:  OK

CheckDir: pwOmics.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/pwOmics.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.12.0’
* 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 251.636  1.111 253.966
* 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-3.7-bioc/meat/pwOmics.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pwOmics
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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 Oct 16 23:31:53 2018 
*********************************************** 
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 
  5.502   0.337   6.308 

name	user	system	elapsed
clusterTimeProfiles	0.003	0.001	0.004
consDynamicNet	0.003	0.000	0.004
findSignalingAxes	0.003	0.000	0.003
generate_DSSignalingBase	0.003	0.000	0.004
getBiopaxModel	0.004	0.001	0.004
getDS_PWs	0.003	0.000	0.004
getDS_TFs	0.003	0.000	0.004
getDS_TGs	0.003	0.001	0.004
getGenesIntersection	0.003	0.000	0.003
getOmicsDataset	0.002	0.000	0.003
getOmicsTimepoints	0.001	0.000	0.001
getOmicsallGeneIDs	0.002	0.000	0.002
getOmicsallProteinIDs	0.002	0.000	0.002
getProteinIntersection	0.003	0.000	0.004
getTFIntersection	0.003	0.001	0.004
getUS_PWs	0.002	0.000	0.002
getUS_TFs	0.002	0.001	0.003
getUS_regulators	0.002	0.000	0.003
get_matching_transcripts	0.003	0.001	0.004
gettpIntersection	0.003	0.000	0.004
identifyPR	0.002	0.000	0.002
identifyPWTFTGs	0.002	0.000	0.002
identifyPWs	0.003	0.001	0.004
identifyRsofTFs	0.004	0.001	0.004
identifyTFs	0.002	0.000	0.002
infoConsensusGraph	0.003	0.001	0.004
plotConsDynNet	0.003	0.001	0.004
plotConsensusGraph	0.003	0.000	0.004
plotConsensusProfiles	0.002	0.001	0.002
plotTimeProfileClusters	0.003	0.000	0.004
readOmics	0.001	0.001	0.002
readPWdata	0.001	0.000	0.002
readPhosphodata	0.002	0.000	0.002
readTFdata	0.002	0.000	0.002
staticConsensusNet	0.003	0.000	0.004
temp_correlations	251.636	1.111	253.966