CRAN Package Check Results for Package MetaPCA

Last updated on 2015-08-02 06:48:02.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.4 0.64 10.74 11.38 NOTE
r-devel-linux-x86_64-debian-gcc 0.1.4 0.65 10.79 11.44 NOTE
r-devel-linux-x86_64-fedora-clang 0.1.4 21.52 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.4 20.17 NOTE
r-devel-osx-x86_64-clang 0.1.4 22.41 NOTE
r-devel-windows-ix86+x86_64 0.1.4 3.00 20.00 23.00 NOTE
r-patched-linux-x86_64 0.1.4 0.64 10.82 11.46 NOTE
r-patched-solaris-sparc 0.1.4 143.70 NOTE
r-patched-solaris-x86 0.1.4 30.30 NOTE
r-release-linux-x86_64 0.1.4 0.64 11.28 11.92 NOTE
r-release-osx-x86_64-mavericks 0.1.4 NOTE
r-release-windows-ix86+x86_64 0.1.4 4.00 32.00 36.00 NOTE
r-oldrel-windows-ix86+x86_64 0.1.4 4.00 26.00 30.00 NOTE

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-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.
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-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 binding for global variable ‘IQR’
    DropDupGenes: no visible global function definition for ‘stopWorkers’
    MetaPCA: no visible global function definition for ‘PCAgrid’
    MetaPCA: no visible global function definition for ‘cov’
    PlotPC2D: no visible global function definition for ‘quartz’
    PlotPC2D: no visible global function definition for ‘X11’
    PlotPC2D: no visible global function definition for ‘cov.mve’
    PlotPC2D: no visible global function definition for ‘ellipse’
    PlotPC2D: no visible global function definition for ‘plot’
    PlotPC2D: no visible global function definition for ‘lines’
    PlotPC2D: no visible global function definition for ‘points’
    PlotPC2D: no visible global function definition for ‘axis’
    PlotPC2D: no visible global function definition for ‘box’
    PlotPC2D: no visible global function definition for ‘abline’
    PlotPC2D: no visible global function definition for ‘legend’
    PlotPC2D: no visible global function definition for ‘title’
    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
     ‘na.omit’
    PreprocessMetaAnalysis: no visible global function definition for
     ‘impute.knn’
    legend2: no visible global function definition for ‘par’
    legend2: no visible global function definition for ‘as.graphicsAnnot’
    legend2: no visible global function definition for ‘xy.coords’
    legend2 : rect2: no visible global function definition for ‘rect’
    legend2 : segments2: no visible global function definition for
     ‘segments’
    legend2 : points2: no visible global function definition for ‘points’
    legend2 : text2: no visible global function definition for ‘text’
    legend2: no visible global function definition for ‘strwidth’
    legend2: no visible global function definition for ‘xinch’
    legend2: no visible global function definition for ‘yinch’
    legend2: no visible global function definition for ‘strheight’
    requireAll: no visible global function definition for
     ‘installed.packages’
    requireAll: no visible global function definition for ‘biocLite’
    Undefined global functions or variables:
     %do% %dopar% IQR PCAgrid X11 abline as.graphicsAnnot axis biocLite
     box cov cov.mve dat ellipse foreach impute.knn installed.packages
     iter legend lines na.omit par plot points quartz rect registerDoMC
     registerDoSMP segments startWorkers stopWorkers strheight strwidth
     text title xinch xy.coords yinch
    Consider adding
     importFrom("grDevices", "X11", "as.graphicsAnnot", "quartz",
     "xy.coords")
     importFrom("graphics", "abline", "axis", "box", "legend", "lines",
     "par", "plot", "points", "rect", "segments", "strheight",
     "strwidth", "text", "title", "xinch", "yinch")
     importFrom("stats", "IQR", "cov", "na.omit")
     importFrom("utils", "installed.packages")
    to your NAMESPACE.
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

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-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: 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: 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’
    Undefined global functions or variables:
     %do% %dopar% PCAgrid biocLite cov.mve dat ellipse foreach impute.knn
     iter registerDoMC registerDoSMP startWorkers stopWorkers
Flavor: r-devel-osx-x86_64-clang

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 binding for global variable 'IQR'
    DropDupGenes: no visible global function definition for 'stopWorkers'
    MetaPCA: no visible global function definition for 'PCAgrid'
    MetaPCA: no visible global function definition for 'cov'
    PlotPC2D: no visible global function definition for 'windows'
    PlotPC2D: no visible global function definition for 'X11'
    PlotPC2D: no visible global function definition for 'cov.mve'
    PlotPC2D: no visible global function definition for 'ellipse'
    PlotPC2D: no visible global function definition for 'plot'
    PlotPC2D: no visible global function definition for 'lines'
    PlotPC2D: no visible global function definition for 'points'
    PlotPC2D: no visible global function definition for 'axis'
    PlotPC2D: no visible global function definition for 'box'
    PlotPC2D: no visible global function definition for 'abline'
    PlotPC2D: no visible global function definition for 'legend'
    PlotPC2D: no visible global function definition for 'title'
    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
     'na.omit'
    PreprocessMetaAnalysis: no visible global function definition for
     'impute.knn'
    legend2: no visible global function definition for 'par'
    legend2: no visible global function definition for 'as.graphicsAnnot'
    legend2: no visible global function definition for 'xy.coords'
    legend2 : rect2: no visible global function definition for 'rect'
    legend2 : segments2: no visible global function definition for
     'segments'
    legend2 : points2: no visible global function definition for 'points'
    legend2 : text2: no visible global function definition for 'text'
    legend2: no visible global function definition for 'strwidth'
    legend2: no visible global function definition for 'xinch'
    legend2: no visible global function definition for 'yinch'
    legend2: no visible global function definition for 'strheight'
    requireAll: no visible global function definition for
     'installed.packages'
    requireAll: no visible global function definition for 'biocLite'
    Undefined global functions or variables:
     %do% %dopar% IQR PCAgrid X11 abline as.graphicsAnnot axis biocLite
     box cov cov.mve dat ellipse foreach impute.knn installed.packages
     iter legend lines na.omit par plot points rect registerDoMC
     registerDoSMP segments startWorkers stopWorkers strheight strwidth
     text title windows xinch xy.coords yinch
    Consider adding
     importFrom("grDevices", "X11", "as.graphicsAnnot", "windows",
     "xy.coords")
     importFrom("graphics", "abline", "axis", "box", "legend", "lines",
     "par", "plot", "points", "rect", "segments", "strheight",
     "strwidth", "text", "title", "xinch", "yinch")
     importFrom("stats", "IQR", "cov", "na.omit")
     importFrom("utils", "installed.packages")
    to your NAMESPACE.
Flavor: r-devel-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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.1.4
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Flavor: r-release-osx-x86_64-mavericks

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-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64