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BioC 3.5: CHECK report for DrugVsDisease on tokay2

This page was generated on 2017-10-18 14:22:20 -0400 (Wed, 18 Oct 2017).

Package 368/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DrugVsDisease 2.16.0
j. Saez-Rodriguez
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/DrugVsDisease
Branch: RELEASE_3_5
Last Commit: f45a703
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DrugVsDisease
Version: 2.16.0
Command: rm -rf DrugVsDisease.buildbin-libdir DrugVsDisease.Rcheck && mkdir DrugVsDisease.buildbin-libdir DrugVsDisease.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DrugVsDisease.buildbin-libdir DrugVsDisease_2.16.0.tar.gz >DrugVsDisease.Rcheck\00install.out 2>&1 && cp DrugVsDisease.Rcheck\00install.out DrugVsDisease-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=DrugVsDisease.buildbin-libdir --install="check:DrugVsDisease-install.out" --force-multiarch --no-vignettes --timings DrugVsDisease_2.16.0.tar.gz
StartedAt: 2017-10-17 23:25:38 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:34:36 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 537.4 seconds
RetCode: 0
Status:  OK  
CheckDir: DrugVsDisease.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   rm -rf DrugVsDisease.buildbin-libdir DrugVsDisease.Rcheck && mkdir DrugVsDisease.buildbin-libdir DrugVsDisease.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DrugVsDisease.buildbin-libdir DrugVsDisease_2.16.0.tar.gz >DrugVsDisease.Rcheck\00install.out 2>&1 && cp DrugVsDisease.Rcheck\00install.out DrugVsDisease-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=DrugVsDisease.buildbin-libdir --install="check:DrugVsDisease-install.out" --force-multiarch --no-vignettes --timings DrugVsDisease_2.16.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/DrugVsDisease.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '2.16.0'
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
DrugVsDisease-package 28.77   4.10   60.57
classifyprofile       18.13   3.76   21.89
selectrankedlists     16.03   0.77   16.80
generateprofiles       8.47   0.00   34.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
DrugVsDisease-package 28.12   1.99   49.83
classifyprofile       15.46   2.29   17.75
selectrankedlists     13.49   0.97   14.45
generateprofiles       6.75   0.00   45.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/DrugVsDisease.Rcheck/00check.log'
for details.


DrugVsDisease.Rcheck/00install.out:


install for i386

* installing *source* package 'DrugVsDisease' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'

install for x64

* installing *source* package 'DrugVsDisease' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
* MD5 sums
packaged installation of 'DrugVsDisease' as DrugVsDisease_2.16.0.zip
* DONE (DrugVsDisease)

DrugVsDisease.Rcheck/examples_i386/DrugVsDisease-Ex.timings:

nameusersystemelapsed
DrugVsDisease-package28.77 4.1060.57
classifyprofile18.13 3.7621.89
customClust000
customdb0.020.000.01
customedge000
customsif0.010.000.02
generateprofiles 8.47 0.0034.14
profiles000
selectrankedlists16.03 0.7716.80
selprofile0.020.000.01

DrugVsDisease.Rcheck/examples_x64/DrugVsDisease-Ex.timings:

nameusersystemelapsed
DrugVsDisease-package28.12 1.9949.83
classifyprofile15.46 2.2917.75
customClust0.000.020.02
customdb000
customedge000
customsif000
generateprofiles 6.75 0.0045.30
profiles000
selectrankedlists13.49 0.9714.45
selprofile0.010.000.02