Back to Multiple platform build/check report for BioC 3.13
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CHECK report for cummeRbund on malbec2

This page was generated on 2021-01-17 12:31:34 -0500 (Sun, 17 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE cummeRbund PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 407/1931HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cummeRbund 2.33.0
Loyal A. Goff
Snapshot Date: 2021-01-16 14:40:27 -0500 (Sat, 16 Jan 2021)
URL: https://git.bioconductor.org/packages/cummeRbund
Branch: master
Last Commit: 7d5cb76
Last Changed Date: 2020-10-27 10:43:08 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: cummeRbund
Version: 2.33.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cummeRbund.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cummeRbund_2.33.0.tar.gz
StartedAt: 2021-01-17 00:37:30 -0500 (Sun, 17 Jan 2021)
EndedAt: 2021-01-17 00:44:03 -0500 (Sun, 17 Jan 2021)
EllapsedTime: 393.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: cummeRbund.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cummeRbund.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cummeRbund_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cummeRbund.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘2.33.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cummeRbund’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    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.
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 ... 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-3.13-bioc/meat/cummeRbund.Rcheck/00check.log’
for details.



Installation output

cummeRbund.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cummeRbund
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘cummeRbund’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (cummeRbund)

Tests output


Example timings

cummeRbund.Rcheck/cummeRbund-Ex.timings

nameusersystemelapsed
CuffData-class0.0010.0000.002
CuffDist-class0.0000.0010.001
CuffFeature-class0.0010.0000.001
CuffFeatureSet-class0.0000.0000.001
CuffGene-class0.0000.0000.001
CuffGeneSet-class0.0000.0000.001
CuffSet-class0.0000.0000.001
JSdist0.0010.0000.001
JSdistFromP0.0010.0000.000
JSdistVec0.0010.0000.000
MAplot3.5200.0403.747
PINK10.0090.0040.013
QCplots0.4400.0120.453
addFeatures000
count0.0150.0000.015
countMatrix0.0280.0000.028
csBoxplot0.3780.0400.417
csCluster0.0470.0040.051
csClusterPlot0.9830.0841.067
csDendro0.0290.0000.029
csDensity0.4290.0360.464
csDistHeat0.2810.0080.289
csHeatmap0.2520.0000.253
csScatter0.3340.0040.338
csSpecificity0.0190.0000.019
csVolcano0.2950.0000.296
diffData0.0120.0000.011
dimensionality0.8460.0040.851
dispersionPlot0.4850.0000.485
distValues0.0540.0360.089
exploratory0.1020.0040.124
expressionBarplot0.7710.0040.775
expressionPlot0.9180.0000.917
featureNames0.0090.0040.014
features0.0170.0000.017
findGene0.0340.0000.033
findSimilar1.5700.0201.591
fpkm0.0120.0000.012
fpkmMatrix0.0250.0000.024
getFeatures0.0260.0000.026
getGene0.1440.0040.149
getGeneId0.0560.0000.056
getGenes0.1200.0040.124
getSig0.020.000.02
getSigTable0.020.000.02
makeprobs0.0010.0000.000
makeprobsvec0.0010.0000.000
readCufflinks0.0110.0000.011
repFpkm0.0140.0000.014
replicates0.0130.0000.013
runInfo0.0130.0000.013
sampleGeneSet0.0110.0000.011
sampleIDs0.0110.0000.011
samples0.0130.0000.013
shannon.entropy000
sigMatrix0.2810.0000.281