CRAN Package Check Results for Package MetaPCA

Last updated on 2014-11-24 23:47:08.

Check Details

Version: 0.1.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘doSMP’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64

Version: 0.1.4
Check: dependencies in R code
Result: NOTE
    Package in Depends field not imported from: ‘foreach’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    ':::' calls which should be '::':
     ‘pcaPP:::l1median_HoCr’ ‘pcaPP:::l1median_VaZh’
     See the note in ?`:::` about the use of this operator.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.4
Check: R code for possible problems
Result: NOTE
    Found an obsolete/platform-specific call in the following function:
     ‘PlotPC2D’
    Found the platform-specific devices:
     ‘X11’ ‘quartz’ ‘windows’
    dev.new() is the preferred way to open a new device, in the unlikely
    event one is needed.
    .MetaSparsePCA: no visible global function definition for ‘%do%’
    .MetaSparsePCA: no visible global function definition for ‘foreach’
    .MetaSparsePCA: no visible global function definition for ‘iter’
    DropDupGenes: no visible global function definition for ‘registerDoMC’
    DropDupGenes: no visible global function definition for ‘startWorkers’
    DropDupGenes: no visible global function definition for ‘registerDoSMP’
    DropDupGenes: no visible global function definition for ‘%dopar%’
    DropDupGenes: no visible global function definition for ‘foreach’
    DropDupGenes: no visible global function definition for ‘iter’
    DropDupGenes: no visible global function definition for ‘stopWorkers’
    MetaPCA: no visible global function definition for ‘PCAgrid’
    PlotPC2D: no visible global function definition for ‘cov.mve’
    PlotPC2D: no visible global function definition for ‘ellipse’
    PreprocessMetaAnalysis: no visible global function definition for
     ‘%do%’
    PreprocessMetaAnalysis: no visible global function definition for
     ‘foreach’
    PreprocessMetaAnalysis: no visible global function definition for
     ‘iter’
    PreprocessMetaAnalysis: no visible binding for global variable ‘dat’
    PreprocessMetaAnalysis: no visible global function definition for
     ‘impute.knn’
    requireAll: no visible global function definition for ‘biocLite’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64

Version: 0.1.4
Check: Rd files
Result: NOTE
    prepare_Rd: DropDupGenes.Rd:29-31: Dropping empty section \details
    prepare_Rd: DropDupGenes.Rd:41-43: Dropping empty section \note
    prepare_Rd: DropDupGenes.Rd:47-49: Dropping empty section \seealso
    prepare_Rd: MetaPCA-package.Rd:29-30: Dropping empty section \seealso
    prepare_Rd: MetaPCA.Rd:76-78: Dropping empty section \details
    prepare_Rd: MetaPCA.Rd:88-90: Dropping empty section \note
    prepare_Rd: MetaPCA.Rd:94-96: Dropping empty section \seealso
    prepare_Rd: PlotPC2D.Rd:80-82: Dropping empty section \details
    prepare_Rd: PlotPC2D.Rd:92-94: Dropping empty section \note
    prepare_Rd: PlotPC2D.Rd:98-100: Dropping empty section \seealso
    prepare_Rd: PreprocessMetaAnalysis.Rd:39-41: Dropping empty section \details
    prepare_Rd: PreprocessMetaAnalysis.Rd:51-53: Dropping empty section \note
    prepare_Rd: PreprocessMetaAnalysis.Rd:57-59: Dropping empty section \seealso
    prepare_Rd: requireAll.Rd:19-21: Dropping empty section \details
    prepare_Rd: requireAll.Rd:31-33: Dropping empty section \note
    prepare_Rd: requireAll.Rd:25-27: Dropping empty section \references
    prepare_Rd: requireAll.Rd:37-39: Dropping empty section \seealso
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.4
Check: Rd line widths
Result: NOTE
    Rd file 'MetaPCA-package.Rd':
     \examples lines wider than 100 characters:
     plot(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], type="n", xlab="", ylab="", xaxt="n", yaxt="n")
     text(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], 1:nrow(metaPC$x[[i]]$coord), cex=1.5)
     PlotPC2D(coord[,1:2], drawEllipse=F, dataset.name="Prostate", .class.order=c("Metastasis","Primary","Normal"),
     .class2=rep(names(metaPC$x), times=sapply(metaPC$x,function(x)nrow(x$coord))),
     #In the case of "SparseAngle" method, the top contributing genes for all studies can be determined
    
    Rd file 'MetaPCA.Rd':
     \usage lines wider than 90 characters:
     MetaPCA(DList, method=c("Angle","Eigen","RobustAngle","SparseAngle"), robust.var=c("qn","mad"), nPC=2,
     .weight=rep(1/length(DList),length(DList)), sparse.maxFeatures=NULL, sparse.lambda=NULL,
     sparse.max.iter=100, sparse.eps=1e-3, .scale=FALSE, .scaleAdjust=TRUE, doPreprocess=TRUE,
     cutRatioByMean=.4, cutRatioByVar=.4, doImpute=TRUE, na.rm.pct=.1, na.rm.pct.each=.5,
     \examples lines wider than 100 characters:
     plot(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], type="n", xlab="", ylab="", xaxt="n", yaxt="n")
     text(metaPC$x[[i]]$coord[,1], metaPC$x[[i]]$coord[,2], 1:nrow(metaPC$x[[i]]$coord), cex=1.5)
     PlotPC2D(coord[,1:2], drawEllipse=F, dataset.name="Prostate", .class.order=c("Metastasis","Primary","Normal"),
     .class2=rep(names(metaPC$x), times=sapply(metaPC$x,function(x)nrow(x$coord))),
     #In the case of "SparseAngle" method, the top contributing genes for all studies can be determined
    
    Rd file 'PlotPC2D.Rd':
     \usage lines wider than 90 characters:
     .points.size=1, .class=rownames(coord), .class.order=NULL, .class.color=NULL,
     .legend=c("bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"))
     \examples lines wider than 100 characters:
     PlotPC2D(coord[,1:2], drawEllipse=T, dataset.name="Prostate", .class.order=c("Metastasis","Primary","Normal"),
     .class2=rep(names(metaPC$x), times=sapply(metaPC$x,function(x)nrow(x$coord))),
    
    Rd file 'PreprocessMetaAnalysis.Rd':
     \usage lines wider than 90 characters:
     PreprocessMetaAnalysis(DList, cutRatioByMean=.4, cutRatioByVar=.4, doImpute=FALSE, na.rm.pct=.1, na.rm.pct.each=.5, verbose=FALSE)
     \examples lines wider than 100 characters:
     DList <- PreprocessMetaAnalysis(list(Yu=Yu, Lapointe=Lapointe, Tomlins=Tomlins, Varambally=Varambally),
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'doMC' 'doSMP'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.4
Check: R code for possible problems
Result: NOTE
    .MetaSparsePCA: no visible global function definition for '%do%'
    .MetaSparsePCA: no visible global function definition for 'foreach'
    .MetaSparsePCA: no visible global function definition for 'iter'
    DropDupGenes: no visible global function definition for 'registerDoMC'
    DropDupGenes: no visible global function definition for 'startWorkers'
    DropDupGenes: no visible global function definition for 'registerDoSMP'
    DropDupGenes: no visible global function definition for '%dopar%'
    DropDupGenes: no visible global function definition for 'foreach'
    DropDupGenes: no visible global function definition for 'iter'
    DropDupGenes: no visible global function definition for 'stopWorkers'
    MetaPCA: no visible global function definition for 'PCAgrid'
    PlotPC2D: no visible global function definition for 'cov.mve'
    PlotPC2D: no visible global function definition for 'ellipse'
    PreprocessMetaAnalysis: no visible global function definition for
     '%do%'
    PreprocessMetaAnalysis: no visible global function definition for
     'foreach'
    PreprocessMetaAnalysis: no visible global function definition for
     'iter'
    PreprocessMetaAnalysis: no visible binding for global variable 'dat'
    PreprocessMetaAnalysis: no visible global function definition for
     'impute.knn'
    requireAll: no visible global function definition for 'biocLite'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.1.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘GEOquery’ ‘affy’ ‘hgu133plus2.db’ ‘doSMP’ ‘impute’
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 0.1.4
Check: R code for possible problems
Result: NOTE
    DropDupGenes: no visible global function definition for ‘startWorkers’
    DropDupGenes: no visible global function definition for ‘registerDoSMP’
    DropDupGenes: no visible global function definition for ‘stopWorkers’
    PreprocessMetaAnalysis: no visible binding for global variable ‘dat’
    PreprocessMetaAnalysis: no visible global function definition for
     ‘impute.knn’
    requireAll: no visible global function definition for ‘biocLite’
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 0.1.4
Check: dependencies in R code
Result: NOTE
    ':::' calls which should be '::':
     'pcaPP:::l1median_HoCr' 'pcaPP:::l1median_VaZh'
     See the note in ?`:::` about the use of this operator.
    See the information on DESCRIPTION files in the chapter 'Creating R
    packages' of the 'Writing R Extensions' manual.
Flavor: r-release-osx-x86_64-snowleopard

Version: 0.1.4
Check: R code for possible problems
Result: NOTE
    Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
     call: match.arg(synchronous, c("off", "normal", "full"))
     error: 'arg' must be NULL or a character vector
    .MetaSparsePCA: no visible global function definition for 'iter'
    DropDupGenes: no visible global function definition for 'registerDoMC'
    DropDupGenes: no visible global function definition for 'startWorkers'
    DropDupGenes: no visible global function definition for 'registerDoSMP'
    DropDupGenes: no visible global function definition for 'iter'
    DropDupGenes: no visible global function definition for 'stopWorkers'
    PreprocessMetaAnalysis: no visible global function definition for
     'iter'
    PreprocessMetaAnalysis: no visible binding for global variable 'dat'
    requireAll: no visible global function definition for 'biocLite'
Flavor: r-oldrel-windows-ix86+x86_64