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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cummeRbund.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings cummeRbund_2.30.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/cummeRbund.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.30.0'
* 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  7.4Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    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.
Namespace in Imports field not imported from: 'S4Vectors'
  All declared Imports should be used.
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 'Rle'
.as.GRanges: no visible global function definition for 'IRanges'
.as.GRanges: no visible global function definition for
  'elementMetadata'
.as.GRanges: no visible global function definition for
  'elementMetadata<-'
.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 'values'
.cuff2db: no visible global function definition for 'seqnames'
.cuff2db: no visible global function definition for 'start'
.cuff2db: no visible global function definition for 'strand'
.cuff2db: no visible global function definition for 'ranges'
.cuff2db: no visible global function definition for 'end'
.cuff2db: no visible global function definition for 'elementNROWS'
.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'
.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'
.fpkmMatrix: no visible global function definition for 'melt'
.fpkmMatrix: no visible global function definition for 'dcast'
.fpkmSCVPlot : <anonymous>: no visible global function definition for
  'sd'
.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
  'Rle'
coerce,CuffGene-GRanges: no visible global function definition for
  'IRanges'
coerce,CuffGene-GRanges: no visible global function definition for
  'elementMetadata'
coerce,CuffGene-GRanges: no visible global function definition for
  'elementMetadata<-'
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,CuffFeatureSet: no visible global function definition for
  'as.dendrogram'
csDendro,CuffFeatureSet: no visible global function definition for
  'hclust'
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 : <anonymous>: no visible global function
  definition for 'sd'
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 Rle 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 elementMetadata elementMetadata<- elementNROWS
  element_blank element_line element_rect element_text end
  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 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 sd seqnames
  significant start stat_density stat_smooth stat_sum stat_summary
  stdev str_split_fixed strand theme theme_bw toJSON tracking_id tracks
  unit v1 v2 value values variable varnames write.table x xlab xlim y
  ylab
Consider adding
  importFrom("stats", "as.dendrogram", "as.dist", "as.formula",
             "cmdscale", "dist", "end", "hclust", "order.dendrogram",
             "p.adjust", "prcomp", "sd", "start")
  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 ... WARNING
Documented arguments not in \usage in documentation object 'diffData':
  '...'

Documented arguments not in \usage in documentation object 'distValues':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
MAplot 2.75   0.19   13.95
** 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: 1 WARNING, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/cummeRbund_2.30.0.tar.gz && rm -rf cummeRbund.buildbin-libdir && mkdir cummeRbund.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cummeRbund.buildbin-libdir cummeRbund_2.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL cummeRbund_2.30.0.zip && rm cummeRbund_2.30.0.tar.gz cummeRbund_2.30.0.zip
###
##############################################################################
##############################################################################


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                                 Dload  Upload   Total   Spent    Left  Speed

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100 1336k  100 1336k    0     0  9742k      0 --:--:-- --:--:-- --:--:--  9.9M

install for i386

* installing *source* package 'cummeRbund' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cummeRbund'
    finding HTML links ... done
    CuffData-class                          html  
    CuffDist-class                          html  
    CuffFeature-class                       html  
    CuffFeatureSet-class                    html  
    CuffGene-class                          html  
    CuffGeneSet-class                       html  
    CuffSet-class                           html  
    JSdist                                  html  
    JSdistFromP                             html  
    JSdistVec                               html  
    MAplot                                  html  
    PINK1                                   html  
    QCplots                                 html  
    addFeatures                             html  
    count                                   html  
    countMatrix                             html  
    csBoxplot                               html  
    csCluster                               html  
    csClusterPlot                           html  
    csDendro                                html  
    csDensity                               html  
    csDistHeat                              html  
    csHeatmap                               html  
    csScatter                               html  
    csSpecificity                           html  
    csVolcano                               html  
    cummeRbund-package                      html  
    diffData                                html  
    dimensionality                          html  
    dispersionPlot                          html  
    distValues                              html  
    exploratory                             html  
    expressionBarplot                       html  
    expressionPlot                          html  
    featureNames                            html  
    features                                html  
    findGene                                html  
    findSimilar                             html  
    fpkm                                    html  
    fpkmMatrix                              html  
    getFeatures                             html  
    getGene                                 html  
    getGeneId                               html  
    getGenes                                html  
    getLevels                               html  
    getRepLevels                            html  
    getSig                                  html  
    getSigTable                             html  
    makeprobs                               html  
    makeprobsvec                            html  
    readCufflinks                           html  
    repFpkm                                 html  
    replicates                              html  
    runInfo                                 html  
    sampleGeneSet                           html  
    sampleIDs                               html  
    samples                                 html  
    shannon.entropy                         html  
    sigMatrix                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'cummeRbund' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cummeRbund' as cummeRbund_2.30.0.zip
* DONE (cummeRbund)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'cummeRbund' successfully unpacked and MD5 sums checked