Package: DrugVsDisease

Version: 2.24.2

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_2.24.2.tar.gz

StartedAt: 2019-04-15 23:39:01 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:43:09 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 248.6 seconds

RetCode: 0

Status:  OK

CheckDir: DrugVsDisease.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:DrugVsDisease.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DrugVsDisease_2.24.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DrugVsDisease.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.24.2’
* 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
classifyprofile   23.173  5.778  29.176
selectrankedlists 16.688  5.809  22.686
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/DrugVsDisease.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 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)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> require("DrugVsDisease")||stop("unable to load DrugVsDisease")
Loading required package: DrugVsDisease
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data

Attaching package: 'cMap2data'

The following object is masked from 'package:DrugVsDiseasedata':

    genelist

Loading required package: qvalue
[1] TRUE
> library(BiocGenerics)
> library(RUnit)
> BiocGenerics:::testPackage("DrugVsDisease")


RUNIT TEST PROTOCOL -- Mon Apr 15 23:43:04 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 11.592   0.643  12.303 

name	user	system	elapsed
DrugVsDisease-package	0.000	0.000	0.001
classifyprofile	23.173	5.778	29.176
customClust	0.002	0.002	0.003
customdb	0.002	0.002	0.004
customedge	0.002	0.002	0.004
customsif	0.002	0.002	0.004
generateprofiles	0.001	0.000	0.000
profiles	0.002	0.002	0.004
selectrankedlists	16.688	5.809	22.686
selprofile	0.002	0.001	0.004