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BioC 3.2: CHECK report for cummeRbund on zin1

This page was generated on 2016-04-23 10:12:11 -0700 (Sat, 23 Apr 2016).

Package 242/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cummeRbund 2.12.1
Loyal A. Goff
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/cummeRbund
Last Changed Rev: 113113 / Revision: 116712
Last Changed Date: 2016-01-30 16:36:05 -0800 (Sat, 30 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cummeRbund
Version: 2.12.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cummeRbund_2.12.1.tar.gz
StartedAt: 2016-04-22 23:45:41 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:49:50 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 248.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cummeRbund.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings cummeRbund_2.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/cummeRbund.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cummeRbund/DESCRIPTION’ ... OK
* this is package ‘cummeRbund’ version ‘2.12.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cummeRbund’ can be installed ... [23s/23s] OK
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   5.6Mb
* 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
* 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 ‘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 ‘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 ‘strand’
.cuff2db: no visible global function definition for ‘ranges’
.cuff2db: no visible global function definition for ‘elementLengths’
.cuff2db: no visible global function definition for ‘makeTxDb’
.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 ‘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 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: 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’
.getSigTable: no visible global function definition for ‘dbGetQuery’
.getSigTable: no visible global function definition for ‘acast’
.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’
.makeRnkTest: no visible global function definition for ‘dbGetQuery’
.makeRnkTestStat: no visible global function definition for
  ‘dbGetQuery’
.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 ‘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 ‘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’
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 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 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 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 ‘make.db.names’
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
  ‘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 : .local: no visible global function definition for
  ‘ggplot’
MAplot,CuffData : .local: no visible global function definition for
  ‘geom_point’
MAplot,CuffData : .local: no visible global function definition for
  ‘aes’
MAplot,CuffData : .local: no visible binding for global variable ‘A’
MAplot,CuffData : .local: no visible binding for global variable ‘M’
MAplot,CuffData : .local: no visible global function definition for
  ‘stat_smooth’
MAplot,CuffData : .local: no visible global function definition for
  ‘geom_hline’
MDSplot,CuffData : .local: no visible global function definition for
  ‘ggplot’
MDSplot,CuffData : .local: no visible global function definition for
  ‘geom_point’
MDSplot,CuffData : .local: no visible global function definition for
  ‘aes’
MDSplot,CuffData : .local: no visible binding for global variable ‘M1’
MDSplot,CuffData : .local: no visible binding for global variable ‘M2’
MDSplot,CuffData : .local: no visible global function definition for
  ‘geom_text’
MDSplot,CuffData : .local: no visible global function definition for
  ‘theme_bw’
MDSplot,CuffFeatureSet : .local: no visible global function definition
  for ‘ggplot’
MDSplot,CuffFeatureSet : .local: no visible global function definition
  for ‘geom_point’
MDSplot,CuffFeatureSet : .local: no visible global function definition
  for ‘aes’
MDSplot,CuffFeatureSet : .local: no visible binding for global variable
  ‘M1’
MDSplot,CuffFeatureSet : .local: no visible binding for global variable
  ‘M2’
MDSplot,CuffFeatureSet : .local: no visible global function definition
  for ‘geom_text’
MDSplot,CuffFeatureSet : .local: no visible global function definition
  for ‘theme_bw’
PCAplot,CuffData : .local: no visible global function definition for
  ‘ggplot’
PCAplot,CuffData : .local: no visible global function definition for
  ‘aes_string’
PCAplot,CuffData : .local: no visible global function definition for
  ‘geom_point’
PCAplot,CuffData : .local: no visible global function definition for
  ‘aes’
PCAplot,CuffData : .local: no visible binding for global variable
  ‘obsnames’
PCAplot,CuffData : .local: no visible global function definition for
  ‘geom_hline’
PCAplot,CuffData : .local: no visible global function definition for
  ‘geom_vline’
PCAplot,CuffData : .local: no visible global function definition for
  ‘geom_text’
PCAplot,CuffData : .local: no visible binding for global variable ‘v1’
PCAplot,CuffData : .local: no visible binding for global variable ‘v2’
PCAplot,CuffData : .local: no visible binding for global variable
  ‘varnames’
PCAplot,CuffData : .local: no visible global function definition for
  ‘geom_segment’
PCAplot,CuffData : .local: no visible global function definition for
  ‘arrow’
PCAplot,CuffData : .local: no visible global function definition for
  ‘unit’
PCAplot,CuffData : .local: no visible global function definition for
  ‘theme_bw’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘ggplot’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘aes_string’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘geom_point’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘aes’
PCAplot,CuffFeatureSet : .local: no visible binding for global variable
  ‘obsnames’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘geom_hline’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘geom_vline’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘geom_text’
PCAplot,CuffFeatureSet : .local: no visible binding for global variable
  ‘v1’
PCAplot,CuffFeatureSet : .local: no visible binding for global variable
  ‘v2’
PCAplot,CuffFeatureSet : .local: no visible binding for global variable
  ‘varnames’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘geom_segment’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘arrow’
PCAplot,CuffFeatureSet : .local: no visible global function definition
  for ‘unit’
PCAplot,CuffFeatureSet : .local: 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 : .local: no visible global function definition for
  ‘make.db.names’
addFeatures,CuffSet : .local: no visible global function definition for
  ‘dbWriteTable’
addFeatures,CuffSet : .local: no visible global function definition for
  ‘dbGetQuery’
annotation,CuffData : .local: 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 : .local: no visible global function definition for
  ‘dbGetQuery’
countMatrix,CuffData : .local: no visible global function definition
  for ‘dbGetQuery’
countMatrix,CuffFeatureSet : .local: no visible global function
  definition for ‘melt’
countMatrix,CuffFeatureSet : .local: no visible global function
  definition for ‘dcast’
csBoxplot,CuffData : .local: no visible global function definition for
  ‘ggplot’
csBoxplot,CuffData : .local: no visible global function definition for
  ‘geom_boxplot’
csBoxplot,CuffData : .local: no visible global function definition for
  ‘aes’
csBoxplot,CuffData : .local: no visible binding for global variable
  ‘condition’
csBoxplot,CuffData : .local: no visible global function definition for
  ‘theme’
csBoxplot,CuffData : .local: no visible global function definition for
  ‘element_text’
csBoxplot,CuffData : .local: no visible global function definition for
  ‘scale_fill_hue’
csCluster,CuffFeatureSet : .local: no visible global function
  definition for ‘pam’
csDensity,CuffData : .local: no visible global function definition for
  ‘ggplot’
csDensity,CuffData : .local: no visible global function definition for
  ‘geom_density’
csDensity,CuffData : .local: no visible global function definition for
  ‘aes’
csDensity,CuffData : .local: no visible binding for global variable
  ‘condition’
csDensity,CuffData : .local: no visible global function definition for
  ‘labs’
csDensity,CuffData : .local: no visible global function definition for
  ‘scale_fill_hue’
csDensity,CuffData : .local: no visible global function definition for
  ‘scale_color_hue’
csDensity,CuffFeatureSet : .local: no visible global function
  definition for ‘ggplot’
csDensity,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_density’
csDensity,CuffFeatureSet : .local: no visible global function
  definition for ‘aes’
csDensity,CuffFeatureSet : .local: no visible binding for global
  variable ‘condition’
csDensity,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_fill_hue’
csDensity,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_color_hue’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘melt’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘ggplot’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘aes’
csDistHeat,CuffData : .local: no visible binding for global variable
  ‘X1’
csDistHeat,CuffData : .local: no visible binding for global variable
  ‘X2’
csDistHeat,CuffData : .local: no visible binding for global variable
  ‘value’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘geom_tile’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘scale_x_discrete’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘scale_y_discrete’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘theme’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘element_text’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘element_line’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘element_rect’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘scale_fill_gradient’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘scale_fill_gradient2’
csDistHeat,CuffData : .local: no visible global function definition for
  ‘geom_text’
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 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 : .local: no visible global function
  definition for ‘melt’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘ggplot’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_rect’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘aes’
csHeatmap,CuffFeatureSet : .local: no visible binding for global
  variable ‘colInd’
csHeatmap,CuffFeatureSet : .local: no visible binding for global
  variable ‘rowInd’
csHeatmap,CuffFeatureSet : .local: no visible binding for global
  variable ‘value’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_x_continuous’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_y_continuous’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘theme’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘element_blank’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘element_line’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘element_rect’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘element_text’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_fill_gradient’
csHeatmap,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_fill_gradient2’
csNMF,CuffData : .local: no visible global function definition for
  ‘nnmf’
csNMF,CuffFeatureSet : .local: no visible global function definition
  for ‘nnmf’
csPie,CuffGene : .local: no visible global function definition for
  ‘ggplot’
csPie,CuffGene : .local: no visible global function definition for
  ‘aes’
csPie,CuffGene : .local: no visible binding for global variable
  ‘tracking_id’
csPie,CuffGene : .local: no visible global function definition for
  ‘geom_bar’
csPie,CuffGene : .local: no visible global function definition for
  ‘coord_polar’
csPie,CuffGene : .local: no visible global function definition for
  ‘scale_fill_hue’
csPie,CuffGene : .local: no visible global function definition for
  ‘scale_color_hue’
csPie,CuffGene : .local: no visible global function definition for
  ‘theme_bw’
csPie,CuffGene : .local: no visible global function definition for
  ‘facet_wrap’
csPie,CuffGene : .local: no visible global function definition for
  ‘theme’
csPie,CuffGene : .local: no visible global function definition for
  ‘element_blank’
csScatter,CuffData : .local: no visible global function definition for
  ‘str_split_fixed’
csScatter,CuffData : .local: no visible global function definition for
  ‘ggplot’
csScatter,CuffData : .local: no visible global function definition for
  ‘aes_string’
csScatter,CuffData : .local: no visible global function definition for
  ‘geom_point’
csScatter,CuffData : .local: no visible global function definition for
  ‘geom_abline’
csScatter,CuffData : .local: no visible global function definition for
  ‘geom_rug’
csScatter,CuffData : .local: no visible global function definition for
  ‘stat_smooth’
csScatter,CuffData : .local: no visible global function definition for
  ‘geom_text’
csScatter,CuffData : .local: no visible global function definition for
  ‘scale_y_log10’
csScatter,CuffData : .local: no visible global function definition for
  ‘scale_x_log10’
csScatter,CuffData : .local: no visible global function definition for
  ‘labs’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘str_split_fixed’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘ggplot’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘aes_string’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_point’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_abline’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_rug’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘stat_smooth’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_text’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_y_log10’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_x_log10’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘ylab’
csScatter,CuffFeatureSet : .local: no visible global function
  definition for ‘xlab’
csScatterMatrix,CuffData : .local: no visible global function
  definition for ‘geom_abline’
csScatterMatrix,CuffData : .local: no visible global function
  definition for ‘theme_bw’
csScatterMatrix,CuffData : .local: no visible global function
  definition for ‘ylab’
csScatterMatrix,CuffData : .local: no visible global function
  definition for ‘xlab’
csVolcano,CuffData : .local: no visible global function definition for
  ‘ggplot’
csVolcano,CuffData : .local: no visible global function definition for
  ‘geom_point’
csVolcano,CuffData : .local: no visible global function definition for
  ‘aes’
csVolcano,CuffData : .local: no visible binding for global variable
  ‘log2_fold_change’
csVolcano,CuffData : .local: no visible binding for global variable
  ‘p_value’
csVolcano,CuffData : .local: no visible binding for global variable
  ‘significant’
csVolcano,CuffData : .local: no visible global function definition for
  ‘theme_bw’
csVolcano,CuffData : .local: no visible global function definition for
  ‘labs’
csVolcano,CuffData : .local: no visible global function definition for
  ‘scale_colour_manual’
csVolcano,CuffData : .local: no visible global function definition for
  ‘scale_x_continuous’
csVolcano,CuffData : .local: no visible global function definition for
  ‘xlab’
csVolcano,CuffData : .local: no visible global function definition for
  ‘ylab’
csVolcano,CuffFeatureSet : .local: no visible global function
  definition for ‘ggplot’
csVolcano,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_point’
csVolcano,CuffFeatureSet : .local: no visible global function
  definition for ‘aes’
csVolcano,CuffFeatureSet : .local: no visible binding for global
  variable ‘log2_fold_change’
csVolcano,CuffFeatureSet : .local: no visible binding for global
  variable ‘p_value’
csVolcano,CuffFeatureSet : .local: no visible binding for global
  variable ‘significant’
csVolcano,CuffFeatureSet : .local: no visible global function
  definition for ‘labs’
csVolcano,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_x_continuous’
csVolcano,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_colour_manual’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘aes’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘aes_string’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘ggplot’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘geom_point’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘scale_colour_manual’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘facet_grid’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘geom_vline’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘theme_bw’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘xlab’
csVolcanoMatrix,CuffData : .local: no visible global function
  definition for ‘ylab’
diffData,CuffData : .local: no visible global function definition for
  ‘dbGetQuery’
diffTable,CuffData : .local: no visible global function definition for
  ‘melt’
diffTable,CuffData : .local: no visible global function definition for
  ‘dcast’
diffTable,CuffFeatureSet : .local: no visible global function
  definition for ‘melt’
diffTable,CuffFeatureSet : .local: 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 : .local: no visible global function definition for
  ‘dbGetQuery’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘ggplot’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘aes’
expressionBarplot,CuffFeature : .local: no visible binding for global
  variable ‘sample_name’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘geom_bar’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘geom_point’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘geom_errorbar’
expressionBarplot,CuffFeature : .local: no visible binding for global
  variable ‘conf_lo’
expressionBarplot,CuffFeature : .local: no visible binding for global
  variable ‘conf_hi’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘scale_y_log10’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘facet_wrap’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘labs’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘theme’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘element_text’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘ylab’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘geom_text’
expressionBarplot,CuffFeature : .local: no visible binding for global
  variable ‘quant_status’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘scale_fill_hue’
expressionBarplot,CuffFeature : .local: no visible global function
  definition for ‘scale_colour_manual’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘position_dodge’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘ggplot’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘aes’
expressionBarplot,CuffFeatureSet : .local: no visible binding for
  global variable ‘tracking_id’
expressionBarplot,CuffFeatureSet : .local: no visible binding for
  global variable ‘sample_name’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_bar’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_errorbar’
expressionBarplot,CuffFeatureSet : .local: no visible binding for
  global variable ‘conf_lo’
expressionBarplot,CuffFeatureSet : .local: no visible binding for
  global variable ‘conf_hi’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_y_log10’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_text’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_x_discrete’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘theme’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘element_text’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘ylab’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_fill_hue’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_color_hue’
expressionBarplot,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_colour_manual’
expressionPlot,CuffFeature: no visible binding for global variable
  ‘mean_cl_boot’
expressionPlot,CuffFeature : .local: no visible binding for global
  variable ‘mean_cl_boot’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘ggplot’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘geom_line’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘aes’
expressionPlot,CuffFeature : .local: no visible binding for global
  variable ‘sample_name’
expressionPlot,CuffFeature : .local: no visible binding for global
  variable ‘tracking_id’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘geom_point’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘geom_errorbar’
expressionPlot,CuffFeature : .local: no visible binding for global
  variable ‘conf_lo’
expressionPlot,CuffFeature : .local: no visible binding for global
  variable ‘conf_hi’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘scale_y_log10’
expressionPlot,CuffFeature : .local: no visible binding for global
  variable ‘quant_status’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘stat_summary’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘ylab’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘scale_fill_hue’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘scale_color_hue’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘labs’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘theme’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘element_text’
expressionPlot,CuffFeature : .local: no visible global function
  definition for ‘facet_wrap’
expressionPlot,CuffFeatureSet: no visible binding for global variable
  ‘mean_cl_boot’
expressionPlot,CuffFeatureSet : .local: no visible binding for global
  variable ‘mean_cl_boot’
expressionPlot,CuffFeatureSet : .local: no visible global function
  definition for ‘ggplot’
expressionPlot,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_line’
expressionPlot,CuffFeatureSet : .local: no visible global function
  definition for ‘aes’
expressionPlot,CuffFeatureSet : .local: no visible binding for global
  variable ‘sample_name’
expressionPlot,CuffFeatureSet : .local: no visible binding for global
  variable ‘tracking_id’
expressionPlot,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_point’
expressionPlot,CuffFeatureSet : .local: no visible global function
  definition for ‘geom_errorbar’
expressionPlot,CuffFeatureSet : .local: no visible binding for global
  variable ‘conf_lo’
expressionPlot,CuffFeatureSet : .local: no visible binding for global
  variable ‘conf_hi’
expressionPlot,CuffFeatureSet : .local: no visible binding for global
  variable ‘quant_status’
expressionPlot,CuffFeatureSet : .local: no visible global function
  definition for ‘scale_y_log10’
expressionPlot,CuffFeatureSet : .local: no visible global function
  definition for ‘stat_summary’
expressionPlot,CuffFeatureSet : .local: 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 : .local: no visible global function definition for
  ‘dbGetQuery’
fpkmMatrix,CuffData : .local: no visible global function definition for
  ‘dbGetQuery’
fpkmMatrix,CuffFeature : .local: no visible global function definition
  for ‘melt’
fpkmMatrix,CuffFeature : .local: no visible global function definition
  for ‘dcast’
fpkmMatrix,CuffFeatureSet : .local: no visible global function
  definition for ‘melt’
fpkmMatrix,CuffFeatureSet : .local: no visible global function
  definition for ‘dcast’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘melt’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘ggplot’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘aes’
fpkmSCVPlot,CuffData : .local: no visible binding for global variable
  ‘stdev’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘stat_smooth’
fpkmSCVPlot,CuffData : .local: no visible binding for global variable
  ‘sample_name’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘scale_x_log10’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘scale_y_continuous’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘xlab’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘theme_bw’
fpkmSCVPlot,CuffData : .local: no visible global function definition
  for ‘xlim’
fpkmSCVPlot,CuffData : .local: 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 : .local: no visible global function definition for
  ‘dbSendQuery’
getFeatures,CuffSet : .local: 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’
getSigTable,CuffSet: no visible global function definition for
  ‘dbGetQuery’
getSigTable,CuffSet: no visible global function definition for ‘acast’
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’
repCountMatrix,CuffData : .local: no visible global function definition
  for ‘dbGetQuery’
repCountMatrix,CuffFeatureSet : .local: no visible global function
  definition for ‘melt’
repCountMatrix,CuffFeatureSet : .local: no visible global function
  definition for ‘dcast’
repFpkm,CuffData : .local: no visible global function definition for
  ‘dbGetQuery’
repFpkmMatrix,CuffData : .local: no visible global function definition
  for ‘dbGetQuery’
repFpkmMatrix,CuffFeature : .local: no visible global function
  definition for ‘melt’
repFpkmMatrix,CuffFeature : .local: no visible global function
  definition for ‘dcast’
repFpkmMatrix,CuffFeatureSet : .local: no visible global function
  definition for ‘melt’
repFpkmMatrix,CuffFeatureSet : .local: 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 ‘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’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'createDB' but not in code:
  createDB

* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘cummeRbund-manual.pdf’ from 1.5Mb to 1.3Mb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] 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, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/cummeRbund.Rcheck/00check.log’
for details.


cummeRbund.Rcheck/00install.out:

* 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
* DONE (cummeRbund)

cummeRbund.Rcheck/cummeRbund-Ex.timings:

nameusersystemelapsed
CuffData-class0.0010.0000.001
CuffDist-class0.0010.0000.001
CuffFeature-class0.0010.0000.001
CuffFeatureSet-class0.0010.0000.000
CuffGene-class0.0010.0000.001
CuffGeneSet-class0.0010.0000.001
CuffSet-class0.0010.0000.001
JSdist0.0010.0000.002
JSdistFromP0.0010.0000.001
JSdistVec0.0010.0000.001
MAplot1.9220.0201.941
PINK10.0080.0000.008
QCplots0.2720.0120.285
addFeatures000
count0.0100.0000.011
countMatrix0.0170.0040.021
csBoxplot0.2640.0000.263
csCluster0.0370.0000.037
csClusterPlot0.6020.0000.601
csDendro0.0190.0000.019
csDensity0.2430.0000.243
csDistHeat0.6270.0000.626
csHeatmap0.1640.0000.164
csScatter0.2050.0000.205
csSpecificity0.0130.0000.013
csVolcano0.1970.0200.218
diffData0.0070.0000.007
dimensionality0.5130.0160.530
dispersionPlot0.3220.0040.325
distValues0.0540.0120.066
exploratory0.0750.0000.091
expressionBarplot0.5070.0000.511
expressionPlot0.6620.0000.662
featureNames0.0090.0000.009
features0.0110.0000.010
findGene0.0340.0000.034
findSimilar1.0080.0121.019
fpkm0.0090.0000.008
fpkmMatrix0.0180.0000.018
getFeatures0.0160.0000.017
getGene0.1410.0000.141
getGeneId0.0450.0000.045
getGenes0.0780.0040.082
getSig0.0130.0000.013
getSigTable0.0150.0000.015
makeprobs0.0010.0000.001
makeprobsvec0.0010.0000.001
readCufflinks0.0090.0000.009
repFpkm0.010.000.01
replicates0.0050.0040.010
runInfo0.0100.0000.009
sampleGeneSet0.0040.0000.007
sampleIDs0.0060.0000.007
samples0.0060.0040.009
shannon.entropy000
sigMatrix0.2300.0040.234