Package: pwOmics

Version: 1.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pwOmics_1.10.1.tar.gz

StartedAt: 2018-04-12 08:03:21 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:09:34 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 372.4 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 --no-vignettes --timings pwOmics_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/pwOmics.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.1’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘stats’ ‘utils’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SteinerTree_cons: no visible global function definition for ‘na.omit’
clusterTimeProfiles: no visible global function definition for
  ‘na.omit’
consDynamicNet: no visible global function definition for ‘ts’
findSignalingAxes: no visible global function definition for ‘na.omit’
findxneighborsoverlap: no visible global function definition for
  ‘na.omit’
generate_DSSignalingBase: no visible global function definition for
  ‘write.csv’
getAliasfromSTRINGIDs: no visible global function definition for
  ‘na.omit’
getConsensusSTRINGIDs: no visible global function definition for
  ‘na.omit’
getFCsplines: no visible global function definition for ‘smooth.spline’
getGenesIntersection: no visible global function definition for
  ‘na.omit’
getOmicsDataset: no visible global function definition for ‘write.csv’
getProteinIntersection: no visible global function definition for
  ‘na.omit’
getTFIntersection: no visible global function definition for ‘na.omit’
identifyPWTFTGs: no visible binding for global variable ‘upreg’
identifyPWTFTGs: no visible binding for global variable ‘phosphoeffect’
identifyRsofTFs: no visible global function definition for ‘na.omit’
infoConsensusGraph: no visible global function definition for ‘from’
plotConsDynNet: no visible global function definition for ‘pdf’
plotConsDynNet: no visible global function definition for ‘qnorm’
plotConsDynNet: no visible global function definition for ‘dev.off’
plotConsensusGraph: no visible global function definition for ‘pdf’
plotConsensusGraph: no visible global function definition for ‘dev.off’
plotConsensusProfiles: no visible global function definition for ‘pdf’
plotConsensusProfiles: no visible global function definition for
  ‘dev.off’
plotTimeProfileClusters: no visible global function definition for
  ‘pdf’
plotTimeProfileClusters: no visible global function definition for
  ‘rainbow’
plotTimeProfileClusters: no visible global function definition for
  ‘dev.off’
predictFCvals: no visible global function definition for ‘predict’
readPhosphodata: no visible global function definition for ‘read.delim’
readTFtargets: no visible global function definition for ‘read.delim’
selectPWsofTFs: no visible global function definition for ‘na.omit’
staticConsensusNet: no visible global function definition for ‘na.omit’
temp_correlations: no visible global function definition for ‘read.csv’
temp_correlations: no visible global function definition for ‘pdf’
temp_correlations: no visible global function definition for
  ‘colorRampPalette’
temp_correlations: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  colorRampPalette dev.off from na.omit pdf phosphoeffect predict qnorm
  rainbow read.csv read.delim smooth.spline ts upreg write.csv
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("stats", "na.omit", "predict", "qnorm", "smooth.spline",
             "ts")
  importFrom("utils", "read.csv", "read.delim", "write.csv")
to your NAMESPACE file.
* 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 225.74  0.844 230.929
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/pwOmics.Rcheck/00check.log’
for details.

* installing *source* package ‘pwOmics’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pwOmics)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 -- Thu Apr 12 08:09:27 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 
  5.210   0.195   5.841 

name	user	system	elapsed
clusterTimeProfiles	0.001	0.000	0.001
consDynamicNet	0.001	0.000	0.001
findSignalingAxes	0.001	0.000	0.002
generate_DSSignalingBase	0.002	0.000	0.002
getBiopaxModel	0.001	0.000	0.001
getDS_PWs	0.000	0.000	0.001
getDS_TFs	0.001	0.000	0.002
getDS_TGs	0.002	0.001	0.002
getGenesIntersection	0.002	0.001	0.002
getOmicsDataset	0.001	0.000	0.001
getOmicsTimepoints	0	0	0
getOmicsallGeneIDs	0.000	0.001	0.001
getOmicsallProteinIDs	0.001	0.000	0.001
getProteinIntersection	0.001	0.000	0.002
getTFIntersection	0.001	0.000	0.002
getUS_PWs	0.001	0.000	0.001
getUS_TFs	0.002	0.000	0.001
getUS_regulators	0.001	0.000	0.002
get_matching_transcripts	0.001	0.001	0.002
gettpIntersection	0.002	0.000	0.004
identifyPR	0.001	0.001	0.001
identifyPWTFTGs	0.001	0.000	0.002
identifyPWs	0.000	0.000	0.001
identifyRsofTFs	0.001	0.000	0.001
identifyTFs	0.001	0.000	0.001
infoConsensusGraph	0.001	0.001	0.001
plotConsDynNet	0.001	0.000	0.001
plotConsensusGraph	0.001	0.000	0.002
plotConsensusProfiles	0.002	0.000	0.002
plotTimeProfileClusters	0.001	0.000	0.001
readOmics	0	0	0
readPWdata	0.001	0.000	0.001
readPhosphodata	0.000	0.000	0.001
readTFdata	0.000	0.000	0.001
staticConsensusNet	0.001	0.001	0.001
temp_correlations	225.740	0.844	230.929