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CHECK report for DrugVsDisease on tokay2

This page was generated on 2018-10-15 10:16:18 -0400 (Mon, 15 Oct 2018).

Package 413/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DrugVsDisease 2.22.0
j. Saez-Rodriguez
Snapshot Date: 2018-10-14 16:46:11 -0400 (Sun, 14 Oct 2018)
URL: https://git.bioconductor.org/packages/DrugVsDisease
Branch: RELEASE_3_7
Last Commit: a04f774
Last Changed Date: 2018-04-30 10:35:29 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  TIMEOUT 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ TIMEOUT ] OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  TIMEOUT  OK 

Summary

Package: DrugVsDisease
Version: 2.22.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DrugVsDisease_2.22.0.tar.gz
StartedAt: 2018-10-15 01:31:46 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 02:11:47 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 2400.1 seconds
RetCode: None
Status:  TIMEOUT  
CheckDir: DrugVsDisease.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DrugVsDisease_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DrugVsDisease.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ...

Installation output

DrugVsDisease.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/DrugVsDisease_2.22.0.tar.gz && rm -rf DrugVsDisease.buildbin-libdir && mkdir DrugVsDisease.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DrugVsDisease.buildbin-libdir DrugVsDisease_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL DrugVsDisease_2.22.0.zip && rm DrugVsDisease_2.22.0.tar.gz DrugVsDisease_2.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1690k  100 1690k    0     0  18.9M      0 --:--:-- --:--:-- --:--:-- 20.6M

install for i386

* installing *source* package 'DrugVsDisease' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DrugVsDisease'
    finding HTML links ... done
    DrugVsDisease-package                   html  
    classifyprofile                         html  
    combineProfiles                         html  
    customClust                             html  
    customdb                                html  
    customedge                              html  
    customsif                               html  
    generateprofiles                        html  
    profiles                                html  
    selectrankedlists                       html  
    selprofile                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DrugVsDisease' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DrugVsDisease' as DrugVsDisease_2.22.0.zip
* DONE (DrugVsDisease)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'DrugVsDisease' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings