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BioC 3.1: CHECK report for cummeRbund on moscato2

This page was generated on 2015-10-09 09:29:27 -0700 (Fri, 09 Oct 2015).

Package 232/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cummeRbund 2.10.0
Loyal A. Goff
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/cummeRbund
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: cummeRbund
Version: 2.10.0
Command: rm -rf cummeRbund.buildbin-libdir cummeRbund.Rcheck && mkdir cummeRbund.buildbin-libdir cummeRbund.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cummeRbund.buildbin-libdir cummeRbund_2.10.0.tar.gz >cummeRbund.Rcheck\00install.out 2>&1 && cp cummeRbund.Rcheck\00install.out cummeRbund-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cummeRbund.buildbin-libdir --install="check:cummeRbund-install.out" --force-multiarch --no-vignettes --timings cummeRbund_2.10.0.tar.gz
StartedAt: 2015-10-09 00:53:50 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:00:19 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 389.4 seconds
RetCode: 0
Status:  OK  
CheckDir: cummeRbund.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf cummeRbund.buildbin-libdir cummeRbund.Rcheck && mkdir cummeRbund.buildbin-libdir cummeRbund.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cummeRbund.buildbin-libdir cummeRbund_2.10.0.tar.gz >cummeRbund.Rcheck\00install.out 2>&1 && cp cummeRbund.Rcheck\00install.out cummeRbund-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=cummeRbund.buildbin-libdir --install="check:cummeRbund-install.out" --force-multiarch --no-vignettes --timings cummeRbund_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/cummeRbund.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '2.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'RSQLite' 'ggplot2' 'reshape2' 'fastcluster'
  'rtracklayer' 'Gviz'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cummeRbund' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   5.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'plyr'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'NMFN' 'cluster' 'rjson' 'stringr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Gviz' 'RSQLite' 'fastcluster' 'ggplot2' 'reshape2' 'rtracklayer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.CVdensity: no visible global function definition for 'ggplot'
.CVdensity: no visible global function definition for 'geom_density'
.CVdensity: no visible global function definition for 'aes'
.CVdensity: no visible binding for global variable 'CV'
.CVdensity: no visible binding for global variable 'sample_name'
.CVdensity: no visible global function definition for 'scale_x_log10'
.MAplot: no visible global function definition for 'ggplot'
.MAplot: no visible global function definition for 'geom_point'
.MAplot: no visible global function definition for 'aes'
.MAplot: no visible binding for global variable 'A'
.MAplot: no visible binding for global variable 'M'
.MAplot: no visible global function definition for 'stat_smooth'
.MAplot: no visible global function definition for 'geom_hline'
.MDSplot: no visible global function definition for '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 'makeTranscriptDb'
.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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [22s] OK
** running examples for arch 'x64' ... [23s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.


cummeRbund.Rcheck/00install.out:


install for i386

* installing *source* package 'cummeRbund' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'cummeRbund' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'cummeRbund' as cummeRbund_2.10.0.zip
* DONE (cummeRbund)

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

nameusersystemelapsed
CuffData-class000
CuffDist-class000
CuffFeature-class000
CuffFeatureSet-class000
CuffGene-class000
CuffGeneSet-class000
CuffSet-class000
JSdist0.010.000.01
JSdistFromP000
JSdistVec000
MAplot3.420.083.50
PINK10.000.010.01
QCplots0.330.001.07
addFeatures000
count0.010.000.01
countMatrix0.030.000.03
csBoxplot0.280.000.28
csCluster0.050.000.05
csClusterPlot0.780.000.78
csDendro0.020.000.02
csDensity0.250.000.28
csDistHeat0.210.000.21
csHeatmap0.190.000.19
csScatter0.250.000.25
csSpecificity0.020.000.02
csVolcano0.210.000.22
diffData0.020.000.01
dimensionality0.660.000.66
dispersionPlot0.280.000.28
distValues0.060.000.07
exploratory0.160.020.18
expressionBarplot0.530.000.53
expressionPlot0.920.000.92
featureNames0.020.000.02
features0.010.000.02
findGene0.070.000.06
findSimilar1.900.021.92
fpkm000
fpkmMatrix0.010.000.01
getFeatures0.040.000.03
getGene0.210.020.24
getGeneId0.100.000.09
getGenes0.110.000.11
getSig0.010.000.02
getSigTable0.030.000.03
makeprobs000
makeprobsvec000
readCufflinks000
repFpkm000
replicates000
runInfo0.010.000.02
sampleGeneSet0.020.000.01
sampleIDs0.020.000.02
samples000
shannon.entropy000
sigMatrix0.240.000.24

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

nameusersystemelapsed
CuffData-class000
CuffDist-class000
CuffFeature-class000
CuffFeatureSet-class0.010.000.01
CuffGene-class000
CuffGeneSet-class000
CuffSet-class000
JSdist000
JSdistFromP000
JSdistVec000
MAplot0.320.000.31
PINK1000
QCplots0.350.000.36
addFeatures000
count0.000.020.01
countMatrix0.040.000.06
csBoxplot0.700.000.77
csCluster0.040.000.05
csClusterPlot0.830.000.83
csDendro0.020.000.03
csDensity0.330.000.33
csDistHeat0.240.000.25
csHeatmap0.220.000.22
csScatter0.270.000.26
csSpecificity0.020.000.01
csVolcano0.230.000.24
diffData0.020.000.01
dimensionality0.750.000.75
dispersionPlot0.340.020.36
distValues0.050.020.06
exploratory0.120.000.13
expressionBarplot0.600.000.59
expressionPlot0.990.001.00
featureNames0.020.000.01
features0.020.000.02
findGene0.040.000.06
findSimilar1.730.011.75
fpkm0.000.020.01
fpkmMatrix0.030.000.04
getFeatures0.020.000.01
getGene0.190.000.19
getGeneId0.080.000.08
getGenes0.110.000.11
getSig0.020.000.02
getSigTable0.010.000.01
makeprobs000
makeprobsvec000
readCufflinks0.020.000.02
repFpkm0.010.000.01
replicates0.020.000.02
runInfo0.010.000.01
sampleGeneSet000
sampleIDs0.020.000.02
samples0.020.000.02
shannon.entropy000
sigMatrix0.260.000.26