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BioC 3.2: CHECK report for DrugVsDisease on zin1

This page was generated on 2016-04-23 10:12:51 -0700 (Sat, 23 Apr 2016).

Package 290/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DrugVsDisease 2.10.2
j. Saez-Rodriguez
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DrugVsDisease
Last Changed Rev: 112535 / Revision: 116712
Last Changed Date: 2016-01-14 01:19:11 -0800 (Thu, 14 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DrugVsDisease
Version: 2.10.2
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DrugVsDisease_2.10.2.tar.gz
StartedAt: 2016-04-23 00:11:48 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:16:08 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 259.6 seconds
RetCode: 0
Status:  OK 
CheckDir: DrugVsDisease.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings DrugVsDisease_2.10.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/DrugVsDisease.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ‘2.10.2’
* 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 ... [14s/14s] 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 loading without being on the library search path ... 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 binding for global variable ‘drugClusters’
.averagecluster: no visible binding for global variable
  ‘diseaseClusters’
.calculateES: no visible binding for global variable ‘drugRL’
.calculateES: no visible binding for global variable ‘diseaseRL’
.calculateES : <anonymous>: no visible global function definition for
  ‘qvalue’
.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 binding for global variable ‘drugClusters’
.findCluster: no visible binding for global variable ‘diseaseClusters’
.findSignifCompounds: no visible global function definition for
  ‘qvalue’
.fitlms: no visible global function definition for ‘lmFit’
.multcontrast: no visible global function definition for
  ‘contrasts.fit’
.multcontrast: no visible global function definition for ‘eBayes’
.normalisedata: no visible global function definition for ‘rma’
.normalisedata: no visible global function definition for ‘mas5’
.readlocalAE: no visible global function definition for ‘ReadAffy’
.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 binding for global variable ‘drugClusters’
.writecytoscape: no visible binding for global variable ‘cytodrug’
.writecytoscape: no visible binding for global variable ‘druglabels’
.writecytoscape: no visible binding for global variable
  ‘diseaseClusters’
.writecytoscape: no visible binding for global variable ‘cytodisease’
.writecytoscape: no visible binding for global variable ‘diseaselabels’
generateprofiles: no visible binding for global variable ‘genelist’
generateprofiles: no visible global function definition for ‘exprs’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [79s/138s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DrugVsDisease-package 27.716  1.119  58.249
selectrankedlists     19.326  0.416  19.745
classifyprofile       19.176  0.253  19.445
generateprofiles       4.011  0.016  33.635
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/DrugVsDisease.Rcheck/00check.log’
for details.


DrugVsDisease.Rcheck/00install.out:

* installing *source* package ‘DrugVsDisease’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DrugVsDisease)

DrugVsDisease.Rcheck/DrugVsDisease-Ex.timings:

nameusersystemelapsed
DrugVsDisease-package27.716 1.11958.249
classifyprofile19.176 0.25319.445
customClust0.0010.0000.002
customdb0.0020.0000.002
customedge0.0010.0000.001
customsif0.0020.0000.002
generateprofiles 4.011 0.01633.635
profiles0.0010.0000.001
selectrankedlists19.326 0.41619.745
selprofile0.0020.0000.002