maPredictDSC 1.12.0
Adi Laurentiu Tarca
| 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/maPredictDSC | | 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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings maPredictDSC_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/maPredictDSC.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘maPredictDSC/DESCRIPTION’ ... OK
* this is package ‘maPredictDSC’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘MASS’ ‘affy’ ‘limma’ ‘gcrma’ ‘ROC’ ‘class’ ‘e1071’ ‘caret’
‘hgu133plus2.db’ ‘ROCR’ ‘AnnotationDbi’ ‘LungCancerACvsSCCGEO’
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 ‘maPredictDSC’ 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:
‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’ ‘gcrma’ ‘limma’
Please remove these calls from your code.
'library' or 'require' call to ‘parallel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘LungCancerACvsSCCGEO’ ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’
‘gcrma’ ‘hgu133plus2.db’ ‘limma’
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
maPredictDSC: no visible global function definition for
‘installed.packages’
maPredictDSC: no visible global function definition for ‘ReadAffy’
maPredictDSC: no visible global function definition for ‘rma’
maPredictDSC: no visible global function definition for ‘mas5’
maPredictDSC: no visible global function definition for ‘gcrma’
maPredictDSC: no visible global function definition for ‘exprs’
maPredictDSC: no visible global function definition for ‘mas5calls’
maPredictDSC: no visible global function definition for ‘createFolds’
maPredictDSC : mff: no visible global function definition for
‘model.matrix’
maPredictDSC : mff: no visible global function definition for ‘formula’
maPredictDSC : mff: no visible global function definition for ‘lmFit’
maPredictDSC : mff: no visible global function definition for
‘makeContrasts’
maPredictDSC : mff: no visible global function definition for
‘contrasts.fit’
maPredictDSC : mff: no visible global function definition for ‘eBayes’
maPredictDSC : mff: no visible global function definition for
‘topTable’
maPredictDSC : mff: no visible global function definition for ‘pt’
maPredictDSC : mff : wf: no visible global function definition for
‘wilcox.test’
maPredictDSC : mff: no visible global function definition for ‘predict’
maPredictDSC : mff: no visible global function definition for ‘knn’
maPredictDSC : mff: no visible global function definition for ‘svm’
maPredictDSC : mff: no visible global function definition for
‘rocdemo.sca’
maPredictDSC : mff: no visible binding for global variable ‘dxrule.sca’
maPredictDSC : mff: no visible global function definition for ‘AUC’
maPredictDSC: no visible global function definition for ‘mclapply’
maPredictDSC: no visible global function definition for ‘sd’
maPredictDSC: no visible global function definition for ‘model.matrix’
maPredictDSC: no visible global function definition for ‘formula’
maPredictDSC: no visible global function definition for ‘lmFit’
maPredictDSC: no visible global function definition for ‘makeContrasts’
maPredictDSC: no visible global function definition for ‘contrasts.fit’
maPredictDSC: no visible global function definition for ‘eBayes’
maPredictDSC: no visible global function definition for ‘topTable’
maPredictDSC: no visible global function definition for ‘pt’
maPredictDSC : wf: no visible global function definition for
‘wilcox.test’
maPredictDSC: no visible global function definition for ‘predict’
maPredictDSC: no visible global function definition for ‘knn’
maPredictDSC: no visible global function definition for ‘svm’
perfDSC: no visible global function definition for ‘prediction’
perfDSC: no visible global function definition for ‘performance’
perfDSC: no visible global function definition for ‘na.omit’
perfDSC: no visible global function definition for ‘trapezint’
perfDSC: no visible global function definition for ‘rocdemo.sca’
perfDSC: no visible binding for global variable ‘dxrule.sca’
perfDSC: no visible global function definition for ‘AUC’
Undefined global functions or variables:
AUC ReadAffy contrasts.fit createFolds dxrule.sca eBayes exprs
formula gcrma installed.packages knn lmFit makeContrasts mas5
mas5calls mclapply model.matrix na.omit performance predict
prediction pt rma rocdemo.sca sd svm topTable trapezint wilcox.test
Consider adding
importFrom("stats", "formula", "model.matrix", "na.omit", "predict",
"pt", "sd", "wilcox.test")
importFrom("utils", "installed.packages")
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 sizes of PDF files under ‘inst/doc’ ... 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
predictDSC 279.816 13.523 199.369
* 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
‘/Users/biocbuild/bbs-3.4-bioc/meat/maPredictDSC.Rcheck/00check.log’
for details.