cummeRbund 2.8.2
Loyal A. Goff
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/cummeRbund | | Last Changed Rev: 96398 / Revision: 102249 | | Last Changed Date: 2014-11-03 14:15:24 -0800 (Mon, 03 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_2.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/cummeRbund.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cummeRbund/DESCRIPTION’ ... OK
* this is package ‘cummeRbund’ version ‘2.8.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘RSQLite’ ‘ggplot2’ ‘reshape2’ ‘fastcluster’
‘rtracklayer’ ‘Gviz’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
inst/extdata/.RData
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cummeRbund’ can be installed ... [51s/61s] OK
* checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
doc 1.6Mb
extdata 5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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:
‘cluster’ ‘NMFN’ ‘rjson’ ‘stringr’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘fastcluster’ ‘ggplot2’ ‘Gviz’ ‘reshape2’ ‘RSQLite’ ‘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
.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’
.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’
.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’
.makeGeneRegionTrack: no visible global function definition for
‘GeneRegionTrack’
.makeGRanges: no visible global function definition for ‘dbGetQuery’
.makeGRanges: no visible global function definition for ‘GRanges’
.makeGRanges: no visible global function definition for ‘IRanges’
.makeRnk: no visible global function definition for ‘dbGetQuery’
.makeRnkTest: no visible global function definition for ‘dbGetQuery’
.makeRnkTestStat: no visible global function definition for
‘dbGetQuery’
.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’
.nmf: no visible global function definition for ‘nnmf’
.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’
.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..’
.QCTable: no visible global function definition for ‘dbGetQuery’
.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’
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’
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<-’
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’
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’
expressionPlot,CuffFeature: no visible binding for global variable
‘mean_cl_boot’
expressionPlot,CuffFeatureSet: no visible binding for global variable
‘mean_cl_boot’
featureNames,CuffData: no visible global function definition for
‘dbGetQuery’
findGene,CuffSet: no visible global function definition for
‘dbGetQuery’
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’
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’
makeGeneRegionTrack,CuffGene: no visible global function definition for
‘GeneRegionTrack’
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’
makeRnk,CuffData: no visible global function definition for
‘dbGetQuery’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MAplot 4.611 0.176 6.461
* 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
NOTE: There were 6 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/cummeRbund.Rcheck/00check.log’
for details.