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BioC 3.4: CHECK report for cummeRbund on tokay1

This page was generated on 2017-04-15 16:16:55 -0400 (Sat, 15 Apr 2017).

Package 287/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cummeRbund 2.16.0
Loyal A. Goff
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/cummeRbund
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  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cummeRbund
Version: 2.16.0
Command: rm -rf cummeRbund.buildbin-libdir cummeRbund.Rcheck && mkdir cummeRbund.buildbin-libdir cummeRbund.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cummeRbund.buildbin-libdir cummeRbund_2.16.0.tar.gz >cummeRbund.Rcheck\00install.out 2>&1 && cp cummeRbund.Rcheck\00install.out cummeRbund-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=cummeRbund.buildbin-libdir --install="check:cummeRbund-install.out" --force-multiarch --no-vignettes --timings cummeRbund_2.16.0.tar.gz
StartedAt: 2017-04-14 21:47:44 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:54:17 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 393.1 seconds
RetCode: 0
Status:  OK  
CheckDir: cummeRbund.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf cummeRbund.buildbin-libdir cummeRbund.Rcheck && mkdir cummeRbund.buildbin-libdir cummeRbund.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cummeRbund.buildbin-libdir cummeRbund_2.16.0.tar.gz >cummeRbund.Rcheck\00install.out 2>&1 && cp cummeRbund.Rcheck\00install.out cummeRbund-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=cummeRbund.buildbin-libdir --install="check:cummeRbund-install.out" --force-multiarch --no-vignettes --timings cummeRbund_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/cummeRbund.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '2.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'RSQLite' 'ggplot2' 'reshape2' 'fastcluster'
  'rtracklayer' 'Gviz'
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 'cummeRbund' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   5.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'plyr'
A package should be listed in only one of these fields.
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'NMFN' 'cluster' 'rjson' 'stringr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Gviz' 'RSQLite' 'fastcluster' 'ggplot2' 'reshape2' 'rtracklayer'
  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
.CVdensity: no visible global function definition for 'ggplot'
.CVdensity: no visible global function definition for 'geom_density'
.CVdensity: no visible global function definition for 'aes'
.CVdensity: no visible binding for global variable 'CV'
.CVdensity: no visible binding for global variable 'sample_name'
.CVdensity: no visible global function definition for 'scale_x_log10'
.MAplot: no visible global function definition for 'ggplot'
.MAplot: no visible global function definition for 'geom_point'
.MAplot: no visible global function definition for 'aes'
.MAplot: no visible binding for global variable 'A'
.MAplot: no visible binding for global variable 'M'
.MAplot: no visible global function definition for 'stat_smooth'
.MAplot: no visible global function definition for 'geom_hline'
.MDSplot: no visible global function definition for 'cmdscale'
.MDSplot: no visible global function definition for 'ggplot'
.MDSplot: no visible global function definition for 'geom_point'
.MDSplot: no visible global function definition for 'aes'
.MDSplot: no visible binding for global variable 'M1'
.MDSplot: no visible binding for global variable 'M2'
.MDSplot: no visible global function definition for 'geom_text'
.MDSplot: no visible global function definition for 'theme_bw'
.PCAplot: no visible global function definition for 'prcomp'
.PCAplot: no visible global function definition for 'ggplot'
.PCAplot: no visible global function definition for 'aes_string'
.PCAplot: no visible global function definition for 'geom_point'
.PCAplot: no visible global function definition for 'aes'
.PCAplot: no visible binding for global variable 'obsnames'
.PCAplot: no visible global function definition for 'geom_hline'
.PCAplot: no visible global function definition for 'geom_vline'
.PCAplot: no visible global function definition for 'geom_text'
.PCAplot: no visible binding for global variable 'v1'
.PCAplot: no visible binding for global variable 'v2'
.PCAplot: no visible binding for global variable 'varnames'
.PCAplot: no visible global function definition for 'geom_segment'
.PCAplot: no visible global function definition for 'arrow'
.PCAplot: no visible global function definition for 'unit'
.PCAplot: no visible global function definition for 'theme_bw'
.QCTable: no visible global function definition for 'dbGetQuery'
.addFeatures: no visible global function definition for 'make.db.names'
.addFeatures: no visible global function definition for 'dbWriteTable'
.addFeatures: no visible global function definition for 'dbGetQuery'
.as.GRanges: no visible global function definition for 'GRanges'
.as.GRanges: no visible global function definition for 'IRanges'
.barplot: no visible global function definition for 'ggplot'
.barplot: no visible global function definition for 'aes'
.barplot: no visible binding for global variable 'sample_name'
.barplot: no visible global function definition for 'geom_bar'
.barplot: no visible global function definition for 'geom_point'
.barplot: no visible global function definition for 'geom_errorbar'
.barplot: no visible binding for global variable 'conf_lo'
.barplot: no visible binding for global variable 'conf_hi'
.barplot: no visible global function definition for 'scale_y_log10'
.barplot: no visible global function definition for 'facet_wrap'
.barplot: no visible global function definition for 'labs'
.barplot: no visible global function definition for 'theme'
.barplot: no visible global function definition for 'element_text'
.barplot: no visible global function definition for 'ylab'
.barplot: no visible global function definition for 'geom_text'
.barplot: no visible binding for global variable 'quant_status'
.barplot: no visible global function definition for 'scale_fill_hue'
.barplot: no visible global function definition for
  'scale_colour_manual'
.boxplot: no visible global function definition for 'ggplot'
.boxplot: no visible global function definition for 'geom_boxplot'
.boxplot: no visible global function definition for 'aes'
.boxplot: no visible binding for global variable 'condition'
.boxplot: no visible global function definition for 'theme'
.boxplot: no visible global function definition for 'element_text'
.boxplot: no visible global function definition for 'scale_fill_hue'
.checkReps: no visible global function definition for 'dbReadTable'
.checkSamples: no visible global function definition for 'dbReadTable'
.cluster: no visible global function definition for 'pam'
.confidencePlot: no visible global function definition for 'ggplot'
.confidencePlot: no visible global function definition for 'geom_point'
.confidencePlot: no visible global function definition for 'aes'
.confidencePlot: no visible binding for global variable 'CV'
.confidencePlot: no visible global function definition for
  'geom_smooth'
.confidencePlot: no visible binding for global variable 'sample_name'
.confidencePlot: no visible global function definition for
  'geom_abline'
.confidencePlot: no visible global function definition for
  'scale_color_gradient'
.confidencePlot: no visible global function definition for 'labs'
.countMatrix: no visible global function definition for 'melt'
.countMatrix: no visible global function definition for 'dcast'
.cuff2db: no visible global function definition for 'import'
.cuff2db: no visible global function definition for 'seqnames'
.cuff2db: no visible global function definition for 'strand'
.cuff2db: no visible global function definition for 'ranges'
.cuff2db: no visible global function definition for 'makeTxDb'
.dendro: no visible global function definition for 'as.dendrogram'
.dendro: no visible global function definition for 'hclust'
.dendro: no visible global function definition for 'plot'
.density: no visible global function definition for 'ggplot'
.density: no visible global function definition for 'geom_density'
.density: no visible global function definition for 'aes'
.density: no visible binding for global variable 'condition'
.density: no visible global function definition for 'scale_fill_hue'
.density: no visible global function definition for 'scale_color_hue'
.diffTable: no visible global function definition for 'melt'
.diffTable: no visible global function definition for 'dcast'
.dispersionPlot: no visible global function definition for 'ggplot'
.dispersionPlot: no visible global function definition for 'geom_point'
.dispersionPlot: no visible global function definition for 'aes'
.dispersionPlot: no visible binding for global variable 'dispersion'
.dispersionPlot: no visible binding for global variable 'sample_name'
.dispersionPlot: no visible global function definition for 'facet_wrap'
.dispersionPlot: no visible global function definition for
  'scale_x_log10'
.dispersionPlot: no visible global function definition for
  'scale_y_log10'
.distheat: no visible global function definition for 'hclust'
.distheat: no visible global function definition for 'melt'
.distheat: no visible global function definition for 'ggplot'
.distheat: no visible global function definition for 'aes'
.distheat: no visible binding for global variable 'X1'
.distheat: no visible binding for global variable 'X2'
.distheat: no visible binding for global variable 'value'
.distheat: no visible global function definition for 'geom_tile'
.distheat: no visible global function definition for 'scale_x_discrete'
.distheat: no visible global function definition for 'scale_y_discrete'
.distheat: no visible global function definition for 'theme'
.distheat: no visible global function definition for 'element_text'
.distheat: no visible global function definition for 'element_line'
.distheat: no visible global function definition for 'element_rect'
.distheat: no visible global function definition for
  'scale_fill_gradient'
.distheat: no visible global function definition for
  'scale_fill_gradient2'
.distheat: no visible global function definition for 'geom_text'
.expressionPlot: no visible binding for global variable 'mean_cl_boot'
.expressionPlot: no visible global function definition for 'ggplot'
.expressionPlot: no visible global function definition for 'geom_line'
.expressionPlot: no visible global function definition for 'aes'
.expressionPlot: no visible binding for global variable 'sample_name'
.expressionPlot: no visible binding for global variable 'tracking_id'
.expressionPlot: no visible global function definition for 'geom_point'
.expressionPlot: no visible global function definition for
  'geom_errorbar'
.expressionPlot: no visible binding for global variable 'conf_lo'
.expressionPlot: no visible binding for global variable 'conf_hi'
.expressionPlot: no visible global function definition for
  'scale_y_log10'
.expressionPlot: no visible binding for global variable 'quant_status'
.expressionPlot: no visible global function definition for
  'stat_summary'
.expressionPlot: no visible global function definition for 'ylab'
.expressionPlot: no visible global function definition for
  'scale_fill_hue'
.expressionPlot: no visible global function definition for
  'scale_color_hue'
.expressionPlot: no visible global function definition for 'labs'
.expressionPlot: no visible global function definition for 'theme'
.expressionPlot: no visible global function definition for
  'element_text'
.expressionPlot: no visible global function definition for 'facet_wrap'
.fcheatmap: no visible binding for global variable 'dist'
.fcheatmap: no visible global function definition for 'hclust'
.fcheatmap: no visible global function definition for 'melt'
.fcheatmap: no visible global function definition for 'ggplot'
.fcheatmap: no visible global function definition for 'geom_rect'
.fcheatmap: no visible global function definition for 'aes'
.fcheatmap: no visible binding for global variable 'colInd'
.fcheatmap: no visible binding for global variable 'rowInd'
.fcheatmap: no visible binding for global variable 'value'
.fcheatmap: no visible global function definition for
  'scale_x_continuous'
.fcheatmap: no visible global function definition for
  'scale_y_continuous'
.fcheatmap: no visible global function definition for 'theme'
.fcheatmap: no visible global function definition for 'element_blank'
.fcheatmap: no visible global function definition for 'element_line'
.fcheatmap: no visible global function definition for 'element_rect'
.fcheatmap: no visible global function definition for 'element_text'
.fcheatmap: no visible global function definition for
  'scale_fill_gradient'
.fcheatmap: no visible global function definition for
  'scale_fill_gradient2'
.findGene: no visible global function definition for 'dbGetQuery'
.findK: no visible global function definition for 'pam'
.findK: no visible global function definition for 'plot'
.fpkmMatrix: no visible global function definition for 'melt'
.fpkmMatrix: no visible global function definition for 'dcast'
.fpkmSCVPlot: no visible global function definition for 'melt'
.fpkmSCVPlot: no visible global function definition for 'ggplot'
.fpkmSCVPlot: no visible global function definition for 'aes'
.fpkmSCVPlot: no visible binding for global variable 'stdev'
.fpkmSCVPlot: no visible global function definition for 'stat_smooth'
.fpkmSCVPlot: no visible binding for global variable 'sample_name'
.fpkmSCVPlot: no visible global function definition for 'scale_x_log10'
.fpkmSCVPlot: no visible global function definition for
  'scale_y_continuous'
.fpkmSCVPlot: no visible global function definition for 'xlab'
.fpkmSCVPlot: no visible global function definition for 'theme_bw'
.fpkmSCVPlot: no visible global function definition for 'xlim'
.fpkmSCVPlot: no visible global function definition for 'labs'
.getCountMA: no visible global function definition for 'dbGetQuery'
.getFeatures: no visible global function definition for 'dbSendQuery'
.getFeatures: no visible global function definition for 'dbGetQuery'
.getGene: no visible global function definition for 'dbSendQuery'
.getGene: no visible global function definition for 'dbGetQuery'
.getGeneId: no visible global function definition for 'dbGetQuery'
.getGenes: no visible global function definition for 'dbSendQuery'
.getGenes: no visible global function definition for 'dbGetQuery'
.getGenome: no visible global function definition for 'dbGetQuery'
.getLevels: no visible global function definition for 'dbGetQuery'
.getMA: no visible global function definition for 'dbGetQuery'
.getRepConditionLevels: no visible global function definition for
  'dbGetQuery'
.getRepLevels: no visible global function definition for 'dbGetQuery'
.getSig: no visible global function definition for 'dbGetQuery'
.getSig: no visible global function definition for 'p.adjust'
.getSigTable: no visible global function definition for 'dbGetQuery'
.getSigTable: no visible global function definition for 'p.adjust'
.getSigTable: no visible global function definition for 'acast'
.getSigTable: no visible global function definition for 'as.formula'
.ggheat: no visible global function definition for 'hclust'
.ggheat: no visible global function definition for 'melt'
.ggheat: no visible global function definition for 'ggplot'
.ggheat: no visible global function definition for 'geom_rect'
.ggheat: no visible global function definition for 'aes'
.ggheat: no visible binding for global variable 'colInd'
.ggheat: no visible binding for global variable 'rowInd'
.ggheat: no visible binding for global variable 'value'
.ggheat: no visible global function definition for 'scale_x_continuous'
.ggheat: no visible global function definition for 'scale_y_continuous'
.ggheat: no visible global function definition for 'theme'
.ggheat: no visible global function definition for 'element_blank'
.ggheat: no visible global function definition for 'element_line'
.ggheat: no visible global function definition for 'element_rect'
.ggheat: no visible global function definition for 'element_text'
.ggheat: no visible global function definition for
  'scale_fill_gradient'
.ggheat: no visible global function definition for
  'scale_fill_gradient2'
.hclustToJSON: no visible global function definition for 'toJSON'
.heatmap: no visible global function definition for 'ggplot'
.heatmap: no visible global function definition for 'geom_tile'
.heatmap: no visible global function definition for 'aes'
.heatmap: no visible binding for global variable 'tracking_id'
.heatmap: no visible binding for global variable 'sample_name'
.heatmap: no visible global function definition for
  'scale_fill_gradient'
.heatmap: no visible global function definition for 'theme'
.heatmap: no visible global function definition for 'element_text'
.ideogram: no visible global function definition for 'plotIdeogram'
.loadGTF: no visible global function definition for 'import'
.loadGTF: no visible global function definition for 'dbWriteTable'
.makeGRanges: no visible global function definition for 'dbGetQuery'
.makeGRanges: no visible global function definition for 'GRanges'
.makeGRanges: no visible global function definition for 'IRanges'
.makeGeneRegionTrack: no visible global function definition for
  'GeneRegionTrack'
.makeRnk: no visible global function definition for 'dbGetQuery'
.makeRnk: no visible global function definition for 'write.table'
.makeRnkTest: no visible global function definition for 'dbGetQuery'
.makeRnkTest: no visible global function definition for 'write.table'
.makeRnkTestStat: no visible global function definition for
  'dbGetQuery'
.makeRnkTestStat: no visible global function definition for
  'write.table'
.nmf: no visible global function definition for 'nnmf'
.pie: no visible global function definition for 'ggplot'
.pie: no visible global function definition for 'aes'
.pie: no visible binding for global variable 'tracking_id'
.pie: no visible global function definition for 'geom_bar'
.pie: no visible global function definition for 'coord_polar'
.pie: no visible global function definition for 'scale_fill_hue'
.pie: no visible global function definition for 'scale_color_hue'
.pie: no visible global function definition for 'theme_bw'
.pie: no visible global function definition for 'facet_wrap'
.pie: no visible global function definition for 'theme'
.pie: no visible global function definition for 'element_blank'
.plot: no visible global function definition for 'IdeogramTrack'
.plot: no visible global function definition for 'GenomeAxisTrack'
.plot: no visible global function definition for
  'BiomartGeneRegionTrack'
.plot: no visible global function definition for 'plotTracks'
.plot2: no visible global function definition for 'theme_bw'
.plot2: no visible global function definition for 'theme'
.plot2: no visible global function definition for 'hasAxis<-'
.plot2: no visible global function definition for 'ggplot'
.plot2: no visible global function definition for 'tracks'
.plotmatrix: no visible global function definition for 'aes'
.plotmatrix: no visible binding for global variable 'x'
.plotmatrix: no visible binding for global variable 'y'
.plotmatrix: no visible global function definition for 'aes_string'
.plotmatrix: no visible global function definition for 'ggplot'
.plotmatrix: no visible global function definition for 'facet_grid'
.plotmatrix: no visible global function definition for 'geom_hex'
.plotmatrix: no visible global function definition for 'geom_point'
.plotmatrix: no visible global function definition for 'stat_density'
.plotmatrix: no visible binding for global variable '..scaled..'
.ratioCluster: no visible global function definition for 'dist'
.ratioCluster: no visible global function definition for 'pam'
.recordGenome: no visible global function definition for 'dbSendQuery'
.repCountMatrix: no visible global function definition for 'melt'
.repCountMatrix: no visible global function definition for 'dcast'
.repFpkmMatrix: no visible global function definition for 'melt'
.repFpkmMatrix: no visible global function definition for 'dcast'
.runInfo: no visible global function definition for 'dbGetQuery'
.scatter: no visible global function definition for 'str_split_fixed'
.scatter: no visible global function definition for 'ggplot'
.scatter: no visible global function definition for 'aes_string'
.scatter: no visible global function definition for 'geom_point'
.scatter: no visible global function definition for 'geom_abline'
.scatter: no visible global function definition for 'geom_rug'
.scatter: no visible global function definition for 'stat_smooth'
.scatter: no visible global function definition for 'geom_text'
.scatter: no visible global function definition for 'scale_y_log10'
.scatter: no visible global function definition for 'scale_x_log10'
.scatter: no visible global function definition for 'ylab'
.scatter: no visible global function definition for 'xlab'
.scatter2: no visible global function definition for 'dbGetQuery'
.scatter2: no visible global function definition for 'ggplot'
.scatter2: no visible global function definition for 'theme_bw'
.scatter2: no visible global function definition for 'aes_string'
.scatter2: no visible global function definition for 'geom_point'
.scatter2: no visible global function definition for 'aes'
.scatter2: no visible binding for global variable 'significant'
.scatter2: no visible global function definition for
  'scale_color_manual'
.scatter2: no visible global function definition for 'geom_abline'
.scatter2: no visible global function definition for 'geom_rug'
.scatter2: no visible global function definition for 'stat_smooth'
.scatter2: no visible global function definition for 'geom_text'
.scatter2: no visible global function definition for 'scale_y_log10'
.scatter2: no visible global function definition for 'scale_x_log10'
.scatter2: no visible global function definition for 'labs'
.scatterMat: no visible global function definition for 'geom_abline'
.scatterMat: no visible global function definition for 'theme_bw'
.scatterMat: no visible global function definition for 'ylab'
.scatterMat: no visible global function definition for 'xlab'
.sigMatrix: no visible global function definition for 'dbGetQuery'
.sigMatrix: no visible global function definition for 'p.adjust'
.sigMatrix: no visible global function definition for
  'order.dendrogram'
.sigMatrix: no visible global function definition for 'as.dendrogram'
.sigMatrix: no visible global function definition for 'hclust'
.sigMatrix: no visible global function definition for 'ggplot'
.sigMatrix: no visible global function definition for 'aes'
.sigMatrix: no visible binding for global variable 'sample_1'
.sigMatrix: no visible binding for global variable 'sample_2'
.sigMatrix: no visible global function definition for 'stat_sum'
.sigMatrix: no visible binding for global variable '..n..'
.sigMatrix: no visible global function definition for
  'scale_fill_continuous'
.sigMatrix: no visible global function definition for 'expand_limits'
.sigMatrix: no visible global function definition for 'theme_bw'
.sigMatrix: no visible global function definition for 'labs'
.sigMatrix: no visible global function definition for 'theme'
.sigMatrix: no visible global function definition for 'element_text'
.sigMatrix: no visible global function definition for 'coord_equal'
.statsMatrix: no visible global function definition for 'dbGetQuery'
.values: no visible global function definition for 'dbGetQuery'
.varModel: no visible global function definition for 'dbGetQuery'
.volcano: no visible global function definition for 'ggplot'
.volcano: no visible global function definition for 'geom_point'
.volcano: no visible global function definition for 'aes'
.volcano: no visible binding for global variable 'log2_fold_change'
.volcano: no visible binding for global variable 'p_value'
.volcano: no visible binding for global variable 'significant'
.volcano: no visible global function definition for 'labs'
.volcano: no visible global function definition for
  'scale_x_continuous'
.volcano: no visible global function definition for
  'scale_colour_manual'
.volcanoMatrix: no visible global function definition for 'aes'
.volcanoMatrix: no visible global function definition for 'aes_string'
.volcanoMatrix: no visible global function definition for 'ggplot'
.volcanoMatrix: no visible global function definition for 'geom_point'
.volcanoMatrix: no visible global function definition for
  'scale_colour_manual'
.volcanoMatrix: no visible global function definition for 'facet_grid'
.volcanoMatrix: no visible global function definition for 'geom_vline'
.volcanoMatrix: no visible global function definition for 'theme_bw'
.volcanoMatrix: no visible global function definition for 'xlab'
.volcanoMatrix: no visible global function definition for 'ylab'
JSdist: no visible global function definition for 'as.dist'
bulk_insert: no visible global function definition for 'dbBegin'
bulk_insert: no visible global function definition for
  'dbGetPreparedQuery'
bulk_insert: no visible global function definition for 'dbCommit'
createDB_noIndex: no visible global function definition for 'dbDriver'
createDB_noIndex: no visible global function definition for 'dbConnect'
createDB_noIndex : <anonymous>: no visible global function definition
  for 'dbGetQuery'
createIndices: no visible global function definition for 'dbDriver'
createIndices: no visible global function definition for 'dbConnect'
createIndices : <anonymous>: no visible global function definition for
  'dbGetQuery'
csClusterPlot: no visible binding for global variable 'mean_cl_boot'
csClusterPlot: no visible global function definition for 'melt'
csClusterPlot: no visible global function definition for 'ggplot'
csClusterPlot: no visible global function definition for 'geom_line'
csClusterPlot: no visible global function definition for 'aes'
csClusterPlot: no visible binding for global variable 'variable'
csClusterPlot: no visible binding for global variable 'value'
csClusterPlot: no visible binding for global variable 'cluster'
csClusterPlot: no visible binding for global variable 'ids'
csClusterPlot: no visible global function definition for 'theme_bw'
csClusterPlot: no visible global function definition for 'facet_wrap'
csClusterPlot: no visible global function definition for 'stat_summary'
csClusterPlot: no visible global function definition for
  'scale_y_log10'
csClusterPlot: no visible global function definition for
  'scale_color_hue'
csClusterPlot: no visible global function definition for 'theme'
csClusterPlot: no visible global function definition for 'element_text'
expressionPlot: no visible binding for global variable 'mean_cl_boot'
loadCDS: no visible binding for global variable 'read.table'
loadCDS: no visible global function definition for 'make.db.names'
loadCDS: no visible global function definition for 'dbReadTable'
loadCDS: no visible global function definition for 'melt'
loadCDS: no visible global function definition for 'dcast'
loadGenes: no visible binding for global variable 'read.table'
loadGenes: no visible global function definition for 'make.db.names'
loadGenes: no visible global function definition for 'dbReadTable'
loadGenes: no visible global function definition for 'melt'
loadGenes: no visible global function definition for 'dcast'
loadIsoforms: no visible binding for global variable 'read.table'
loadIsoforms: no visible global function definition for 'make.db.names'
loadIsoforms: no visible global function definition for 'dbReadTable'
loadIsoforms: no visible global function definition for 'melt'
loadIsoforms: no visible global function definition for 'dcast'
loadRepTable: no visible global function definition for 'read.delim'
loadRepTable: no visible global function definition for 'make.db.names'
loadRunInfo: no visible binding for global variable 'read.table'
loadTSS: no visible binding for global variable 'read.table'
loadTSS: no visible global function definition for 'make.db.names'
loadTSS: no visible global function definition for 'dbReadTable'
loadTSS: no visible global function definition for 'melt'
loadTSS: no visible global function definition for 'dcast'
loadVarModelTable: no visible global function definition for
  'read.delim'
loadVarModelTable: no visible global function definition for
  'make.db.names'
populateSampleTable: no visible global function definition for
  'make.db.names'
populateSampleTable: no visible global function definition for
  'dbWriteTable'
readCufflinks: no visible global function definition for 'dbConnect'
readCufflinks: no visible global function definition for 'dbDriver'
MAplot,CuffData: no visible global function definition for 'ggplot'
MAplot,CuffData: no visible global function definition for 'geom_point'
MAplot,CuffData: no visible global function definition for 'aes'
MAplot,CuffData: no visible binding for global variable 'A'
MAplot,CuffData: no visible binding for global variable 'M'
MAplot,CuffData: no visible global function definition for
  'stat_smooth'
MAplot,CuffData: no visible global function definition for 'geom_hline'
MDSplot,CuffData: no visible global function definition for 'cmdscale'
MDSplot,CuffData: no visible global function definition for 'ggplot'
MDSplot,CuffData: no visible global function definition for
  'geom_point'
MDSplot,CuffData: no visible global function definition for 'aes'
MDSplot,CuffData: no visible binding for global variable 'M1'
MDSplot,CuffData: no visible binding for global variable 'M2'
MDSplot,CuffData: no visible global function definition for 'geom_text'
MDSplot,CuffData: no visible global function definition for 'theme_bw'
MDSplot,CuffFeatureSet: no visible global function definition for
  'cmdscale'
MDSplot,CuffFeatureSet: no visible global function definition for
  'ggplot'
MDSplot,CuffFeatureSet: no visible global function definition for
  'geom_point'
MDSplot,CuffFeatureSet: no visible global function definition for 'aes'
MDSplot,CuffFeatureSet: no visible binding for global variable 'M1'
MDSplot,CuffFeatureSet: no visible binding for global variable 'M2'
MDSplot,CuffFeatureSet: no visible global function definition for
  'geom_text'
MDSplot,CuffFeatureSet: no visible global function definition for
  'theme_bw'
PCAplot,CuffData: no visible global function definition for 'prcomp'
PCAplot,CuffData: no visible global function definition for 'ggplot'
PCAplot,CuffData: no visible global function definition for
  'aes_string'
PCAplot,CuffData: no visible global function definition for
  'geom_point'
PCAplot,CuffData: no visible global function definition for 'aes'
PCAplot,CuffData: no visible binding for global variable 'obsnames'
PCAplot,CuffData: no visible global function definition for
  'geom_hline'
PCAplot,CuffData: no visible global function definition for
  'geom_vline'
PCAplot,CuffData: no visible global function definition for 'geom_text'
PCAplot,CuffData: no visible binding for global variable 'v1'
PCAplot,CuffData: no visible binding for global variable 'v2'
PCAplot,CuffData: no visible binding for global variable 'varnames'
PCAplot,CuffData: no visible global function definition for
  'geom_segment'
PCAplot,CuffData: no visible global function definition for 'arrow'
PCAplot,CuffData: no visible global function definition for 'unit'
PCAplot,CuffData: no visible global function definition for 'theme_bw'
PCAplot,CuffFeatureSet: no visible global function definition for
  'prcomp'
PCAplot,CuffFeatureSet: no visible global function definition for
  'ggplot'
PCAplot,CuffFeatureSet: no visible global function definition for
  'aes_string'
PCAplot,CuffFeatureSet: no visible global function definition for
  'geom_point'
PCAplot,CuffFeatureSet: no visible global function definition for 'aes'
PCAplot,CuffFeatureSet: no visible binding for global variable
  'obsnames'
PCAplot,CuffFeatureSet: no visible global function definition for
  'geom_hline'
PCAplot,CuffFeatureSet: no visible global function definition for
  'geom_vline'
PCAplot,CuffFeatureSet: no visible global function definition for
  'geom_text'
PCAplot,CuffFeatureSet: no visible binding for global variable 'v1'
PCAplot,CuffFeatureSet: no visible binding for global variable 'v2'
PCAplot,CuffFeatureSet: no visible binding for global variable
  'varnames'
PCAplot,CuffFeatureSet: no visible global function definition for
  'geom_segment'
PCAplot,CuffFeatureSet: no visible global function definition for
  'arrow'
PCAplot,CuffFeatureSet: no visible global function definition for
  'unit'
PCAplot,CuffFeatureSet: no visible global function definition for
  'theme_bw'
addFeatures,CuffData: no visible global function definition for
  'make.db.names'
addFeatures,CuffData: no visible global function definition for
  'dbWriteTable'
addFeatures,CuffData: no visible global function definition for
  'dbGetQuery'
addFeatures,CuffSet: no visible global function definition for
  'make.db.names'
addFeatures,CuffSet: no visible global function definition for
  'dbWriteTable'
addFeatures,CuffSet: no visible global function definition for
  'dbGetQuery'
annotation,CuffData: no visible global function definition for
  'dbGetQuery'
coerce,CuffGene-GRanges: no visible global function definition for
  'GRanges'
coerce,CuffGene-GRanges: no visible global function definition for
  'IRanges'
count,CuffData: no visible global function definition for 'dbGetQuery'
countMatrix,CuffData: no visible global function definition for
  'dbGetQuery'
countMatrix,CuffFeatureSet: no visible global function definition for
  'melt'
countMatrix,CuffFeatureSet: no visible global function definition for
  'dcast'
csBoxplot,CuffData: no visible global function definition for 'ggplot'
csBoxplot,CuffData: no visible global function definition for
  'geom_boxplot'
csBoxplot,CuffData: no visible global function definition for 'aes'
csBoxplot,CuffData: no visible binding for global variable 'condition'
csBoxplot,CuffData: no visible global function definition for 'theme'
csBoxplot,CuffData: no visible global function definition for
  'element_text'
csBoxplot,CuffData: no visible global function definition for
  'scale_fill_hue'
csCluster,CuffFeatureSet: no visible global function definition for
  'pam'
csDendro,CuffData: no visible global function definition for
  'as.dendrogram'
csDendro,CuffData: no visible global function definition for 'hclust'
csDendro,CuffData: no visible global function definition for 'plot'
csDendro,CuffFeatureSet: no visible global function definition for
  'as.dendrogram'
csDendro,CuffFeatureSet: no visible global function definition for
  'hclust'
csDendro,CuffFeatureSet: no visible global function definition for
  'plot'
csDensity,CuffData: no visible global function definition for 'ggplot'
csDensity,CuffData: no visible global function definition for
  'geom_density'
csDensity,CuffData: no visible global function definition for 'aes'
csDensity,CuffData: no visible binding for global variable 'condition'
csDensity,CuffData: no visible global function definition for 'labs'
csDensity,CuffData: no visible global function definition for
  'scale_fill_hue'
csDensity,CuffData: no visible global function definition for
  'scale_color_hue'
csDensity,CuffFeatureSet: no visible global function definition for
  'ggplot'
csDensity,CuffFeatureSet: no visible global function definition for
  'geom_density'
csDensity,CuffFeatureSet: no visible global function definition for
  'aes'
csDensity,CuffFeatureSet: no visible binding for global variable
  'condition'
csDensity,CuffFeatureSet: no visible global function definition for
  'scale_fill_hue'
csDensity,CuffFeatureSet: no visible global function definition for
  'scale_color_hue'
csDistHeat,CuffData: no visible global function definition for 'hclust'
csDistHeat,CuffData: no visible global function definition for 'melt'
csDistHeat,CuffData: no visible global function definition for 'ggplot'
csDistHeat,CuffData: no visible global function definition for 'aes'
csDistHeat,CuffData: no visible binding for global variable 'X1'
csDistHeat,CuffData: no visible binding for global variable 'X2'
csDistHeat,CuffData: no visible binding for global variable 'value'
csDistHeat,CuffData: no visible global function definition for
  'geom_tile'
csDistHeat,CuffData: no visible global function definition for
  'scale_x_discrete'
csDistHeat,CuffData: no visible global function definition for
  'scale_y_discrete'
csDistHeat,CuffData: no visible global function definition for 'theme'
csDistHeat,CuffData: no visible global function definition for
  'element_text'
csDistHeat,CuffData: no visible global function definition for
  'element_line'
csDistHeat,CuffData: no visible global function definition for
  'element_rect'
csDistHeat,CuffData: no visible global function definition for
  'scale_fill_gradient'
csDistHeat,CuffData: no visible global function definition for
  'scale_fill_gradient2'
csDistHeat,CuffData: no visible global function definition for
  'geom_text'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'hclust'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'melt'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'ggplot'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'aes'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X1'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X2'
csDistHeat,CuffFeatureSet: no visible binding for global variable
  'value'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'geom_tile'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'scale_x_discrete'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'scale_y_discrete'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'theme'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'element_text'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'element_line'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'element_rect'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'scale_fill_gradient'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'scale_fill_gradient2'
csDistHeat,CuffFeatureSet: no visible global function definition for
  'geom_text'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
  variable 'dist'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'hclust'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'melt'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'ggplot'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'geom_rect'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'aes'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
  variable 'colInd'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
  variable 'rowInd'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
  variable 'value'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'scale_x_continuous'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'scale_y_continuous'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'theme'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'element_blank'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'element_line'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'element_rect'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'element_text'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'scale_fill_gradient'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
  definition for 'scale_fill_gradient2'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'hclust'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'melt'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'ggplot'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'geom_rect'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'aes'
csHeatmap,CuffFeatureSet: no visible binding for global variable
  'colInd'
csHeatmap,CuffFeatureSet: no visible binding for global variable
  'rowInd'
csHeatmap,CuffFeatureSet: no visible binding for global variable
  'value'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'scale_x_continuous'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'scale_y_continuous'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'theme'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'element_blank'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'element_line'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'element_rect'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'element_text'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'scale_fill_gradient'
csHeatmap,CuffFeatureSet: no visible global function definition for
  'scale_fill_gradient2'
csNMF,CuffData: no visible global function definition for 'nnmf'
csNMF,CuffFeatureSet: no visible global function definition for 'nnmf'
csPie,CuffGene: no visible global function definition for 'ggplot'
csPie,CuffGene: no visible global function definition for 'aes'
csPie,CuffGene: no visible binding for global variable 'tracking_id'
csPie,CuffGene: no visible global function definition for 'geom_bar'
csPie,CuffGene: no visible global function definition for 'coord_polar'
csPie,CuffGene: no visible global function definition for
  'scale_fill_hue'
csPie,CuffGene: no visible global function definition for
  'scale_color_hue'
csPie,CuffGene: no visible global function definition for 'theme_bw'
csPie,CuffGene: no visible global function definition for 'facet_wrap'
csPie,CuffGene: no visible global function definition for 'theme'
csPie,CuffGene: no visible global function definition for
  'element_blank'
csScatter,CuffData: no visible global function definition for
  'str_split_fixed'
csScatter,CuffData: no visible global function definition for 'ggplot'
csScatter,CuffData: no visible global function definition for
  'aes_string'
csScatter,CuffData: no visible global function definition for
  'geom_point'
csScatter,CuffData: no visible global function definition for
  'geom_abline'
csScatter,CuffData: no visible global function definition for
  'geom_rug'
csScatter,CuffData: no visible global function definition for
  'stat_smooth'
csScatter,CuffData: no visible global function definition for
  'geom_text'
csScatter,CuffData: no visible global function definition for
  'scale_y_log10'
csScatter,CuffData: no visible global function definition for
  'scale_x_log10'
csScatter,CuffData: no visible global function definition for 'labs'
csScatter,CuffFeatureSet: no visible global function definition for
  'str_split_fixed'
csScatter,CuffFeatureSet: no visible global function definition for
  'ggplot'
csScatter,CuffFeatureSet: no visible global function definition for
  'aes_string'
csScatter,CuffFeatureSet: no visible global function definition for
  'geom_point'
csScatter,CuffFeatureSet: no visible global function definition for
  'geom_abline'
csScatter,CuffFeatureSet: no visible global function definition for
  'geom_rug'
csScatter,CuffFeatureSet: no visible global function definition for
  'stat_smooth'
csScatter,CuffFeatureSet: no visible global function definition for
  'geom_text'
csScatter,CuffFeatureSet: no visible global function definition for
  'scale_y_log10'
csScatter,CuffFeatureSet: no visible global function definition for
  'scale_x_log10'
csScatter,CuffFeatureSet: no visible global function definition for
  'ylab'
csScatter,CuffFeatureSet: no visible global function definition for
  'xlab'
csScatterMatrix,CuffData: no visible global function definition for
  'geom_abline'
csScatterMatrix,CuffData: no visible global function definition for
  'theme_bw'
csScatterMatrix,CuffData: no visible global function definition for
  'ylab'
csScatterMatrix,CuffData: no visible global function definition for
  'xlab'
csVolcano,CuffData: no visible global function definition for 'ggplot'
csVolcano,CuffData: no visible global function definition for
  'geom_point'
csVolcano,CuffData: no visible global function definition for 'aes'
csVolcano,CuffData: no visible binding for global variable
  'log2_fold_change'
csVolcano,CuffData: no visible binding for global variable 'p_value'
csVolcano,CuffData: no visible binding for global variable
  'significant'
csVolcano,CuffData: no visible global function definition for
  'theme_bw'
csVolcano,CuffData: no visible global function definition for 'labs'
csVolcano,CuffData: no visible global function definition for
  'scale_colour_manual'
csVolcano,CuffData: no visible global function definition for
  'scale_x_continuous'
csVolcano,CuffData: no visible global function definition for 'xlab'
csVolcano,CuffData: no visible global function definition for 'ylab'
csVolcano,CuffFeatureSet: no visible global function definition for
  'ggplot'
csVolcano,CuffFeatureSet: no visible global function definition for
  'geom_point'
csVolcano,CuffFeatureSet: no visible global function definition for
  'aes'
csVolcano,CuffFeatureSet: no visible binding for global variable
  'log2_fold_change'
csVolcano,CuffFeatureSet: no visible binding for global variable
  'p_value'
csVolcano,CuffFeatureSet: no visible binding for global variable
  'significant'
csVolcano,CuffFeatureSet: no visible global function definition for
  'labs'
csVolcano,CuffFeatureSet: no visible global function definition for
  'scale_x_continuous'
csVolcano,CuffFeatureSet: no visible global function definition for
  'scale_colour_manual'
csVolcanoMatrix,CuffData: no visible global function definition for
  'aes'
csVolcanoMatrix,CuffData: no visible global function definition for
  'aes_string'
csVolcanoMatrix,CuffData: no visible global function definition for
  'ggplot'
csVolcanoMatrix,CuffData: no visible global function definition for
  'geom_point'
csVolcanoMatrix,CuffData: no visible global function definition for
  'scale_colour_manual'
csVolcanoMatrix,CuffData: no visible global function definition for
  'facet_grid'
csVolcanoMatrix,CuffData: no visible global function definition for
  'geom_vline'
csVolcanoMatrix,CuffData: no visible global function definition for
  'theme_bw'
csVolcanoMatrix,CuffData: no visible global function definition for
  'xlab'
csVolcanoMatrix,CuffData: no visible global function definition for
  'ylab'
diffData,CuffData: no visible global function definition for
  'dbGetQuery'
diffTable,CuffData: no visible global function definition for 'melt'
diffTable,CuffData: no visible global function definition for 'dcast'
diffTable,CuffFeatureSet: no visible global function definition for
  'melt'
diffTable,CuffFeatureSet: no visible global function definition for
  'dcast'
dim,CuffData: no visible global function definition for 'dbGetQuery'
dim,CuffDist: no visible global function definition for 'dbGetQuery'
dispersionPlot,CuffData: no visible global function definition for
  'ggplot'
dispersionPlot,CuffData: no visible global function definition for
  'geom_point'
dispersionPlot,CuffData: no visible global function definition for
  'aes'
dispersionPlot,CuffData: no visible binding for global variable
  'dispersion'
dispersionPlot,CuffData: no visible binding for global variable
  'sample_name'
dispersionPlot,CuffData: no visible global function definition for
  'facet_wrap'
dispersionPlot,CuffData: no visible global function definition for
  'scale_x_log10'
dispersionPlot,CuffData: no visible global function definition for
  'scale_y_log10'
dispersionPlot,CuffSet: no visible global function definition for
  'ggplot'
dispersionPlot,CuffSet: no visible global function definition for
  'geom_point'
dispersionPlot,CuffSet: no visible global function definition for 'aes'
dispersionPlot,CuffSet: no visible binding for global variable
  'compatible_count_mean'
dispersionPlot,CuffSet: no visible binding for global variable
  'compatible_count_var'
dispersionPlot,CuffSet: no visible binding for global variable
  'condition'
dispersionPlot,CuffSet: no visible global function definition for
  'geom_line'
dispersionPlot,CuffSet: no visible binding for global variable
  'fitted_var'
dispersionPlot,CuffSet: no visible global function definition for
  'facet_wrap'
dispersionPlot,CuffSet: no visible global function definition for
  'scale_y_log10'
dispersionPlot,CuffSet: no visible global function definition for
  'scale_x_log10'
dispersionPlot,CuffSet: no visible global function definition for
  'theme_bw'
dispersionPlot,CuffSet: no visible global function definition for
  'guides'
distValues,CuffDist: no visible global function definition for
  'dbGetQuery'
expressionBarplot,CuffFeature: no visible global function definition
  for 'ggplot'
expressionBarplot,CuffFeature: no visible global function definition
  for 'aes'
expressionBarplot,CuffFeature: no visible binding for global variable
  'sample_name'
expressionBarplot,CuffFeature: no visible global function definition
  for 'geom_bar'
expressionBarplot,CuffFeature: no visible global function definition
  for 'geom_point'
expressionBarplot,CuffFeature: no visible global function definition
  for 'geom_errorbar'
expressionBarplot,CuffFeature: no visible binding for global variable
  'conf_lo'
expressionBarplot,CuffFeature: no visible binding for global variable
  'conf_hi'
expressionBarplot,CuffFeature: no visible global function definition
  for 'scale_y_log10'
expressionBarplot,CuffFeature: no visible global function definition
  for 'facet_wrap'
expressionBarplot,CuffFeature: no visible global function definition
  for 'labs'
expressionBarplot,CuffFeature: no visible global function definition
  for 'theme'
expressionBarplot,CuffFeature: no visible global function definition
  for 'element_text'
expressionBarplot,CuffFeature: no visible global function definition
  for 'ylab'
expressionBarplot,CuffFeature: no visible global function definition
  for 'geom_text'
expressionBarplot,CuffFeature: no visible binding for global variable
  'quant_status'
expressionBarplot,CuffFeature: no visible global function definition
  for 'scale_fill_hue'
expressionBarplot,CuffFeature: no visible global function definition
  for 'scale_colour_manual'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'position_dodge'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'ggplot'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'aes'
expressionBarplot,CuffFeatureSet: no visible binding for global
  variable 'tracking_id'
expressionBarplot,CuffFeatureSet: no visible binding for global
  variable 'sample_name'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'geom_bar'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'geom_errorbar'
expressionBarplot,CuffFeatureSet: no visible binding for global
  variable 'conf_lo'
expressionBarplot,CuffFeatureSet: no visible binding for global
  variable 'conf_hi'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'scale_y_log10'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'geom_text'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'scale_x_discrete'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'theme'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'element_text'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'ylab'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'scale_fill_hue'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'scale_color_hue'
expressionBarplot,CuffFeatureSet: no visible global function definition
  for 'scale_colour_manual'
expressionPlot,CuffFeature: no visible binding for global variable
  'mean_cl_boot'
expressionPlot,CuffFeature: no visible global function definition for
  'ggplot'
expressionPlot,CuffFeature: no visible global function definition for
  'geom_line'
expressionPlot,CuffFeature: no visible global function definition for
  'aes'
expressionPlot,CuffFeature: no visible binding for global variable
  'sample_name'
expressionPlot,CuffFeature: no visible binding for global variable
  'tracking_id'
expressionPlot,CuffFeature: no visible global function definition for
  'geom_point'
expressionPlot,CuffFeature: no visible global function definition for
  'geom_errorbar'
expressionPlot,CuffFeature: no visible binding for global variable
  'conf_lo'
expressionPlot,CuffFeature: no visible binding for global variable
  'conf_hi'
expressionPlot,CuffFeature: no visible global function definition for
  'scale_y_log10'
expressionPlot,CuffFeature: no visible binding for global variable
  'quant_status'
expressionPlot,CuffFeature: no visible global function definition for
  'stat_summary'
expressionPlot,CuffFeature: no visible global function definition for
  'ylab'
expressionPlot,CuffFeature: no visible global function definition for
  'scale_fill_hue'
expressionPlot,CuffFeature: no visible global function definition for
  'scale_color_hue'
expressionPlot,CuffFeature: no visible global function definition for
  'labs'
expressionPlot,CuffFeature: no visible global function definition for
  'theme'
expressionPlot,CuffFeature: no visible global function definition for
  'element_text'
expressionPlot,CuffFeature: no visible global function definition for
  'facet_wrap'
expressionPlot,CuffFeatureSet: no visible binding for global variable
  'mean_cl_boot'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'ggplot'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'geom_line'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'aes'
expressionPlot,CuffFeatureSet: no visible binding for global variable
  'sample_name'
expressionPlot,CuffFeatureSet: no visible binding for global variable
  'tracking_id'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'geom_point'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'geom_errorbar'
expressionPlot,CuffFeatureSet: no visible binding for global variable
  'conf_lo'
expressionPlot,CuffFeatureSet: no visible binding for global variable
  'conf_hi'
expressionPlot,CuffFeatureSet: no visible binding for global variable
  'quant_status'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'scale_y_log10'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'stat_summary'
expressionPlot,CuffFeatureSet: no visible global function definition
  for 'ylab'
featureNames,CuffData: no visible global function definition for
  'dbGetQuery'
findGene,CuffSet: no visible global function definition for
  'dbGetQuery'
fpkm,CuffData: no visible global function definition for 'dbGetQuery'
fpkmMatrix,CuffData: no visible global function definition for
  'dbGetQuery'
fpkmMatrix,CuffFeature: no visible global function definition for
  'melt'
fpkmMatrix,CuffFeature: no visible global function definition for
  'dcast'
fpkmMatrix,CuffFeatureSet: no visible global function definition for
  'melt'
fpkmMatrix,CuffFeatureSet: no visible global function definition for
  'dcast'
fpkmSCVPlot,CuffData: no visible global function definition for 'melt'
fpkmSCVPlot,CuffData: no visible global function definition for
  'ggplot'
fpkmSCVPlot,CuffData: no visible global function definition for 'aes'
fpkmSCVPlot,CuffData: no visible binding for global variable 'stdev'
fpkmSCVPlot,CuffData: no visible global function definition for
  'stat_smooth'
fpkmSCVPlot,CuffData: no visible binding for global variable
  'sample_name'
fpkmSCVPlot,CuffData: no visible global function definition for
  'scale_x_log10'
fpkmSCVPlot,CuffData: no visible global function definition for
  'scale_y_continuous'
fpkmSCVPlot,CuffData: no visible global function definition for 'xlab'
fpkmSCVPlot,CuffData: no visible global function definition for
  'theme_bw'
fpkmSCVPlot,CuffData: no visible global function definition for 'xlim'
fpkmSCVPlot,CuffData: no visible global function definition for 'labs'
genePlot,CuffGene: no visible global function definition for
  'IdeogramTrack'
genePlot,CuffGene: no visible global function definition for
  'GenomeAxisTrack'
genePlot,CuffGene: no visible global function definition for
  'BiomartGeneRegionTrack'
genePlot,CuffGene: no visible global function definition for
  'plotTracks'
getFeatures,CuffSet: no visible global function definition for
  'dbSendQuery'
getFeatures,CuffSet: no visible global function definition for
  'dbGetQuery'
getGene,CuffSet: no visible global function definition for
  'dbSendQuery'
getGene,CuffSet: no visible global function definition for 'dbGetQuery'
getGeneId,CuffSet: no visible global function definition for
  'dbGetQuery'
getGenes,CuffSet: no visible global function definition for
  'dbSendQuery'
getGenes,CuffSet: no visible global function definition for
  'dbGetQuery'
getLevels,CuffData: no visible global function definition for
  'dbGetQuery'
getLevels,CuffSet: no visible global function definition for
  'dbGetQuery'
getRepLevels,CuffData: no visible global function definition for
  'dbGetQuery'
getRepLevels,CuffSet: no visible global function definition for
  'dbGetQuery'
getSig,CuffSet: no visible global function definition for 'dbGetQuery'
getSig,CuffSet: no visible global function definition for 'p.adjust'
getSigTable,CuffSet: no visible global function definition for
  'dbGetQuery'
getSigTable,CuffSet: no visible global function definition for
  'p.adjust'
getSigTable,CuffSet: no visible global function definition for 'acast'
getSigTable,CuffSet: no visible global function definition for
  'as.formula'
makeGRanges,CuffSet: no visible global function definition for
  'dbGetQuery'
makeGRanges,CuffSet: no visible global function definition for
  'GRanges'
makeGRanges,CuffSet: no visible global function definition for
  'IRanges'
makeGeneRegionTrack,CuffGene: no visible global function definition for
  'GeneRegionTrack'
makeRnk,CuffData: no visible global function definition for
  'dbGetQuery'
makeRnk,CuffData: no visible global function definition for
  'write.table'
repCountMatrix,CuffData: no visible global function definition for
  'dbGetQuery'
repCountMatrix,CuffFeatureSet: no visible global function definition
  for 'melt'
repCountMatrix,CuffFeatureSet: no visible global function definition
  for 'dcast'
repFpkm,CuffData: no visible global function definition for
  'dbGetQuery'
repFpkmMatrix,CuffData: no visible global function definition for
  'dbGetQuery'
repFpkmMatrix,CuffFeature: no visible global function definition for
  'melt'
repFpkmMatrix,CuffFeature: no visible global function definition for
  'dcast'
repFpkmMatrix,CuffFeatureSet: no visible global function definition for
  'melt'
repFpkmMatrix,CuffFeatureSet: no visible global function definition for
  'dcast'
replicates,CuffData: no visible global function definition for
  'dbReadTable'
replicates,CuffSet: no visible global function definition for
  'dbGetQuery'
runInfo,CuffSet: no visible global function definition for 'dbGetQuery'
samples,CuffData: no visible global function definition for
  'dbReadTable'
samples,CuffDist: no visible global function definition for
  'dbReadTable'
samples,CuffSet: no visible global function definition for 'dbGetQuery'
sigMatrix,CuffSet: no visible global function definition for
  'dbGetQuery'
sigMatrix,CuffSet: no visible global function definition for 'p.adjust'
sigMatrix,CuffSet: no visible global function definition for
  'order.dendrogram'
sigMatrix,CuffSet: no visible global function definition for
  'as.dendrogram'
sigMatrix,CuffSet: no visible global function definition for 'hclust'
sigMatrix,CuffSet: no visible global function definition for 'ggplot'
sigMatrix,CuffSet: no visible global function definition for 'aes'
sigMatrix,CuffSet: no visible binding for global variable 'sample_1'
sigMatrix,CuffSet: no visible binding for global variable 'sample_2'
sigMatrix,CuffSet: no visible global function definition for 'stat_sum'
sigMatrix,CuffSet: no visible binding for global variable '..n..'
sigMatrix,CuffSet: no visible global function definition for
  'scale_fill_continuous'
sigMatrix,CuffSet: no visible global function definition for
  'expand_limits'
sigMatrix,CuffSet: no visible global function definition for 'theme_bw'
sigMatrix,CuffSet: no visible global function definition for 'labs'
sigMatrix,CuffSet: no visible global function definition for 'theme'
sigMatrix,CuffSet: no visible global function definition for
  'element_text'
sigMatrix,CuffSet: no visible global function definition for
  'coord_equal'
varModel,CuffSet: no visible global function definition for
  'dbGetQuery'
Undefined global functions or variables:
  ..n.. ..scaled.. A BiomartGeneRegionTrack CV GRanges GeneRegionTrack
  GenomeAxisTrack IRanges IdeogramTrack M M1 M2 X1 X2 acast aes
  aes_string arrow as.dendrogram as.dist as.formula cluster cmdscale
  colInd compatible_count_mean compatible_count_var condition conf_hi
  conf_lo coord_equal coord_polar dbBegin dbCommit dbConnect dbDriver
  dbGetPreparedQuery dbGetQuery dbReadTable dbSendQuery dbWriteTable
  dcast dispersion dist element_blank element_line element_rect
  element_text expand_limits facet_grid facet_wrap fitted_var
  geom_abline geom_bar geom_boxplot geom_density geom_errorbar geom_hex
  geom_hline geom_line geom_point geom_rect geom_rug geom_segment
  geom_smooth geom_text geom_tile geom_vline ggplot guides hasAxis<-
  hclust ids import labs log2_fold_change make.db.names makeTxDb
  mean_cl_boot melt nnmf obsnames order.dendrogram p.adjust p_value pam
  plot plotIdeogram plotTracks position_dodge prcomp quant_status
  ranges read.delim read.table rowInd sample_1 sample_2 sample_name
  scale_color_gradient scale_color_hue scale_color_manual
  scale_colour_manual scale_fill_continuous scale_fill_gradient
  scale_fill_gradient2 scale_fill_hue scale_x_continuous
  scale_x_discrete scale_x_log10 scale_y_continuous scale_y_discrete
  scale_y_log10 seqnames significant stat_density stat_smooth stat_sum
  stat_summary stdev str_split_fixed strand theme theme_bw toJSON
  tracking_id tracks unit v1 v2 value variable varnames write.table x
  xlab xlim y ylab
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.dist", "as.formula",
             "cmdscale", "dist", "hclust", "order.dendrogram",
             "p.adjust", "prcomp")
  importFrom("utils", "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
** running examples for arch 'x64' ... 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.


cummeRbund.Rcheck/00install.out:


install for i386

* installing *source* package 'cummeRbund' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cummeRbund' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cummeRbund' as cummeRbund_2.16.0.zip
* DONE (cummeRbund)

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

nameusersystemelapsed
CuffData-class000
CuffDist-class000
CuffFeature-class000
CuffFeatureSet-class000
CuffGene-class000
CuffGeneSet-class000
CuffSet-class000
JSdist000
JSdistFromP000
JSdistVec000
MAplot2.570.072.66
PINK1000
QCplots0.240.110.34
addFeatures000
count0.000.020.02
countMatrix0.010.010.03
csBoxplot0.210.130.32
csCluster0.010.010.03
csClusterPlot0.660.030.69
csDendro0.010.000.01
csDensity0.250.000.25
csDistHeat0.210.020.22
csHeatmap0.180.010.21
csScatter0.240.000.23
csSpecificity0.010.000.02
csVolcano0.210.020.22
diffData0.010.000.01
dimensionality0.550.000.55
dispersionPlot0.410.010.42
distValues0.040.020.06
exploratory0.080.000.14
expressionBarplot0.560.000.57
expressionPlot0.690.020.70
featureNames0.000.010.01
features0.020.000.02
findGene0.030.000.03
findSimilar0.800.030.83
fpkm0.010.000.01
fpkmMatrix0.020.000.02
getFeatures0.010.000.02
getGene0.110.000.11
getGeneId0.050.000.04
getGenes0.030.050.08
getSig0.020.000.02
getSigTable0.010.000.01
makeprobs000
makeprobsvec000
readCufflinks000
repFpkm0.000.020.02
replicates0.020.000.01
runInfo000
sampleGeneSet0.000.010.02
sampleIDs0.010.000.01
samples0.020.000.02
shannon.entropy000
sigMatrix0.20.00.2

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

nameusersystemelapsed
CuffData-class000
CuffDist-class000
CuffFeature-class000
CuffFeatureSet-class000
CuffGene-class000
CuffGeneSet-class000
CuffSet-class000
JSdist000
JSdistFromP000
JSdistVec000
MAplot0.300.000.29
PINK10.010.000.02
QCplots0.890.000.89
addFeatures000
count0.000.020.02
countMatrix0.030.000.03
csBoxplot0.350.010.36
csCluster0.040.000.04
csClusterPlot0.860.000.86
csDendro0.030.000.03
csDensity0.270.000.27
csDistHeat0.270.000.27
csHeatmap0.230.020.25
csScatter0.270.000.26
csSpecificity0.010.000.02
csVolcano0.270.000.26
diffData0.000.010.02
dimensionality1.260.001.26
dispersionPlot0.500.020.52
distValues0.030.010.05
exploratory0.070.000.07
expressionBarplot0.720.000.72
expressionPlot0.910.000.91
featureNames0.000.020.01
features0.010.000.02
findGene0.030.000.03
findSimilar1.020.021.03
fpkm000
fpkmMatrix0.000.030.03
getFeatures0.020.000.02
getGene0.120.000.12
getGeneId0.030.000.03
getGenes0.10.00.1
getSig0.010.000.01
getSigTable0.020.000.02
makeprobs000
makeprobsvec000
readCufflinks0.010.000.01
repFpkm0.020.000.02
replicates0.010.000.01
runInfo0.020.000.02
sampleGeneSet000
sampleIDs0.000.010.02
samples0.010.000.01
shannon.entropy000
sigMatrix0.290.020.30