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BioC 3.4: CHECK report for DrugVsDisease on malbec1

This page was generated on 2017-04-15 16:11:16 -0400 (Sat, 15 Apr 2017).

Package 346/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DrugVsDisease 2.14.0
j. Saez-Rodriguez
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/DrugVsDisease
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DrugVsDisease
Version: 2.14.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DrugVsDisease_2.14.0.tar.gz
StartedAt: 2017-04-14 22:12:00 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:16:25 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 264.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DrugVsDisease.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DrugVsDisease_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DrugVsDisease.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.14.0’
* 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 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DrugVsDisease-package 24.388  4.376  36.760
classifyprofile       14.020  4.800  18.846
selectrankedlists     12.880  3.360  16.262
generateprofiles       4.536  0.020  28.995
* 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
  ‘/home/biocbuild/bbs-3.4-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-package24.388 4.37636.760
classifyprofile14.020 4.80018.846
customClust0.0000.0000.001
customdb0.0000.0040.001
customedge0.0000.0000.001
customsif0.0040.0000.002
generateprofiles 4.536 0.02028.995
profiles0.0040.0000.001
selectrankedlists12.880 3.36016.262
selprofile0.0000.0000.001