Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-04 11:37:41 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 478/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cummeRbund 2.45.0  (landing page)
Loyal A. Goff
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/cummeRbund
git_branch: devel
git_last_commit: 32af841
git_last_commit_date: 2023-10-24 09:48:13 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for cummeRbund on palomino3


To the developers/maintainers of the cummeRbund package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cummeRbund.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cummeRbund
Version: 2.45.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cummeRbund.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cummeRbund_2.45.0.tar.gz
StartedAt: 2024-03-02 01:45:49 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 01:51:45 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 356.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cummeRbund.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cummeRbund.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings cummeRbund_2.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/cummeRbund.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '2.45.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'RSQLite', 'ggplot2', 'reshape2', 'fastcluster',
  'rtracklayer', 'Gviz'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cummeRbund' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   5.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics' 'plyr'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 Rd file 'diffData.Rd':
  '...'

Documented arguments not in \usage in Rd file 'distValues.Rd':
  '...'

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 ... NOTE
Auto-generated content requiring editing in Rd file 'cummeRbund-package.Rd':
  \references: '~~ Literature or other references for background information ~~'
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'cummeRbund-manual.pdf' from 1.7Mb to 1.5Mb
  consider running tools::compactPDF() on these files,
  or build the source package with --compact-vignettes
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 7 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.



Installation output

cummeRbund.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL cummeRbund
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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-class000
CuffDist-class000
CuffFeature-class000
CuffFeatureSet-class000
CuffGene-class000
CuffGeneSet-class000
CuffSet-class000
JSdist000
JSdistFromP000
JSdistVec000
MAplot1.860.292.95
PINK10.010.000.02
QCplots0.270.010.28
addFeatures000
count0.000.020.01
countMatrix0.020.010.03
csBoxplot1.460.051.52
csCluster0.040.010.05
csClusterPlot0.620.020.64
csDendro0.030.000.03
csDensity0.30.00.3
csDistHeat0.140.090.23
csHeatmap0.200.020.22
csScatter0.330.030.36
csSpecificity0.000.030.04
csVolcano0.220.000.21
diffData0.010.000.02
dimensionality0.520.010.53
dispersionPlot0.410.000.40
distValues0.060.050.11
exploratory0.110.030.15
expressionBarplot0.480.010.50
expressionPlot0.550.020.57
featureNames0.000.030.03
features0.020.000.01
findGene0.010.000.02
findSimilar0.770.020.78
fpkm0.010.000.02
fpkmMatrix0.000.010.01
getFeatures0.010.000.01
getGene0.080.000.08
getGeneId0.020.000.02
getGenes0.090.000.09
getSig0.020.000.02
getSigTable0.010.000.01
makeprobs000
makeprobsvec000
readCufflinks0.020.000.02
repFpkm0.010.000.01
replicates0.020.000.02
runInfo000
sampleGeneSet0.010.000.01
sampleIDs0.000.020.02
samples0.020.000.02
shannon.entropy000
sigMatrix0.310.000.31