DrugVsDisease 2.8.0
j. Saez-Rodriguez
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/DrugVsDisease | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DrugVsDisease_2.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/DrugVsDisease.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.8.0’
* 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 ... [9s/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 ... [70s/120s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DrugVsDisease-package 24.335 0.858 48.913
classifyprofile 17.667 0.715 25.182
selectrankedlists 17.733 0.393 24.430
generateprofiles 4.206 0.119 16.386
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [5s/8s]
[5s/8s] 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-3.1-bioc/meat/DrugVsDisease.Rcheck/00check.log’
for details.
* installing *source* package ‘DrugVsDisease’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DrugVsDisease)