Package: DrugVsDisease

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DrugVsDisease.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DrugVsDisease_2.22.0.tar.gz

StartedAt: 2018-10-15 02:05:05 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 02:45:05 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 2400.2 seconds

RetCode: None

Status:  TIMEOUT

CheckDir: DrugVsDisease.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DrugVsDisease.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DrugVsDisease_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/DrugVsDisease.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 ‘DrugVsDisease/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DrugVsDisease’ version ‘2.22.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘affy’ ‘limma’ ‘biomaRt’ ‘ArrayExpress’ ‘GEOquery’
  ‘DrugVsDiseasedata’ ‘cMap2data’ ‘qvalue’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘DrugVsDisease’ 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
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’
  ‘limma’ ‘qvalue’
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘BiocGenerics’ ‘RUnit’ ‘annotate’ ‘hgu133a.db’ ‘hgu133a2.db’
  ‘hgu133plus2.db’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’
  ‘cMap2data’ ‘limma’ ‘qvalue’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.averagecluster: no visible global function definition for ‘data’
.averagecluster: no visible binding for global variable ‘drugClusters’
.averagecluster: no visible binding for global variable
  ‘diseaseClusters’
.averagecluster: no visible global function definition for ‘median’
.calculateES: no visible binding for global variable ‘drugRL’
.calculateES: no visible binding for global variable ‘diseaseRL’
.calculateES: no visible binding for global variable ‘p.adjust’
.calculateES : <anonymous>: no visible global function definition for
  ‘qvalue’
.combinemed: no visible global function definition for ‘medpolish’
.convertEnsembl: no visible binding for global variable
  ‘annotationlist’
.convertEnsembl: no visible global function definition for ‘useMart’
.convertEnsembl: no visible global function definition for ‘getBM’
.datafromAE: no visible global function definition for ‘ArrayExpress’
.datafromAE: no visible global function definition for ‘annotation’
.datafromAE: no visible global function definition for ‘pData’
.datafromGEO: no visible global function definition for ‘getGEO’
.datafromGEO: no visible global function definition for ‘GDS2eSet’
.datafromGEO: no visible global function definition for ‘pData’
.datafromGEO: no visible global function definition for ‘annotation’
.datafromGEO: no visible binding for global variable ‘GEOfactorvalues’
.datafromGEO: no visible global function definition for ‘exprs’
.findCluster: no visible global function definition for ‘data’
.findCluster: no visible binding for global variable ‘drugClusters’
.findCluster: no visible binding for global variable ‘diseaseClusters’
.findSignifCompounds: no visible global function definition for ‘ecdf’
.findSignifCompounds: no visible global function definition for
  ‘p.adjust’
.findSignifCompounds: no visible global function definition for
  ‘qvalue’
.fitlms: no visible global function definition for ‘read.table’
.fitlms: no visible global function definition for ‘model.matrix’
.fitlms: no visible global function definition for ‘lmFit’
.multcontrast: no visible global function definition for ‘combn’
.multcontrast: no visible global function definition for
  ‘contrasts.fit’
.multcontrast: no visible global function definition for ‘eBayes’
.norm_mrs : <anonymous>: no visible global function definition for
  ‘median’
.normalisedata: no visible global function definition for ‘rma’
.normalisedata: no visible global function definition for ‘mas5’
.ptog: no visible global function definition for ‘setNames’
.readlocalAE: no visible global function definition for ‘ReadAffy’
.readlocalAE: no visible global function definition for ‘read.delim’
.readlocalCEL: no visible global function definition for ‘ReadAffy’
.singlecontrast: no visible global function definition for ‘lmFit’
.singlecontrast: no visible global function definition for
  ‘contrasts.fit’
.singlecontrast: no visible global function definition for ‘eBayes’
.treatmentonlyfit: no visible global function definition for ‘lmFit’
.writecytoscape: no visible global function definition for ‘data’
.writecytoscape: no visible binding for global variable ‘cytodrug’
.writecytoscape: no visible binding for global variable ‘drugClusters’
.writecytoscape: no visible binding for global variable ‘druglabels’
.writecytoscape: no visible binding for global variable ‘cytodisease’
.writecytoscape: no visible binding for global variable
  ‘diseaseClusters’
.writecytoscape: no visible binding for global variable ‘diseaselabels’
.writecytoscape: no visible global function definition for
  ‘write.table’
classifyprofile: no visible global function definition for ‘read.table’
generateprofiles: no visible global function definition for ‘data’
generateprofiles: no visible binding for global variable ‘genelist’
generateprofiles: no visible binding for global variable
  ‘annotationlist’
generateprofiles: no visible global function definition for
  ‘read.table’
generateprofiles: no visible global function definition for ‘exprs’
Undefined global functions or variables:
  ArrayExpress GDS2eSet GEOfactorvalues ReadAffy annotation
  annotationlist combn contrasts.fit cytodisease cytodrug data
  diseaseClusters diseaseRL diseaselabels drugClusters drugRL
  druglabels eBayes ecdf exprs genelist getBM getGEO lmFit mas5 median
  medpolish model.matrix p.adjust pData qvalue read.delim read.table
  rma setNames useMart write.table
Consider adding
  importFrom("stats", "ecdf", "median", "medpolish", "model.matrix",
             "p.adjust", "setNames")
  importFrom("utils", "combn", "data", "read.delim", "read.table",
             "write.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DrugVsDisease
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘DrugVsDisease’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DrugVsDisease)

name	user	system	elapsed
DrugVsDisease-package	45.423	10.042	2113.496
classifyprofile	18.181	5.677	24.093
customClust	0.003	0.002	0.005
customdb	0.002	0.001	0.003
customedge	0.003	0.001	0.004
customsif	0.003	0.001	0.005