| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-29 16:33:42 -0000 (Sun, 29 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4021 |
| 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 | ||||
|
To the developers/maintainers of the cummeRbund package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 448/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cummeRbund 2.41.0 (landing page) Loyal A. Goff
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: cummeRbund |
| Version: 2.41.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cummeRbund.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cummeRbund_2.41.0.tar.gz |
| StartedAt: 2023-01-28 20:53:48 -0000 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 21:02:48 -0000 (Sat, 28 Jan 2023) |
| EllapsedTime: 539.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cummeRbund.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cummeRbund.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings cummeRbund_2.41.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cummeRbund.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cummeRbund/DESCRIPTION’ ... OK
* this is package ‘cummeRbund’ version ‘2.41.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cummeRbund’ can be installed ... OK
* 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 loading without being on the library search path ... WARNING
Error in library(cummeRbund, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘cummeRbund’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'NMFN' 'cluster' 'rjson' 'stringr'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'S4Vectors'
All declared Imports should be used.
Packages in Depends field not imported from:
'Gviz' 'RSQLite' 'fastcluster' 'ggplot2' 'reshape2' 'rtracklayer'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.CVdensity: no visible global function definition for 'ggplot'
.CVdensity: no visible global function definition for 'geom_density'
.CVdensity: no visible global function definition for 'aes'
.CVdensity: no visible binding for global variable 'CV'
.CVdensity: no visible binding for global variable 'sample_name'
.CVdensity: no visible global function definition for 'scale_x_log10'
.MAplot: no visible global function definition for 'ggplot'
.MAplot: no visible global function definition for 'geom_point'
.MAplot: no visible global function definition for 'aes'
.MAplot: no visible binding for global variable 'A'
.MAplot: no visible binding for global variable 'M'
.MAplot: no visible global function definition for 'stat_smooth'
.MAplot: no visible global function definition for 'geom_hline'
.MDSplot: no visible global function definition for 'cmdscale'
.MDSplot: no visible global function definition for 'ggplot'
.MDSplot: no visible global function definition for 'geom_point'
.MDSplot: no visible global function definition for 'aes'
.MDSplot: no visible binding for global variable 'M1'
.MDSplot: no visible binding for global variable 'M2'
.MDSplot: no visible global function definition for 'geom_text'
.MDSplot: no visible global function definition for 'theme_bw'
.PCAplot: no visible global function definition for 'prcomp'
.PCAplot: no visible global function definition for 'ggplot'
.PCAplot: no visible global function definition for 'aes_string'
.PCAplot: no visible global function definition for 'geom_point'
.PCAplot: no visible global function definition for 'aes'
.PCAplot: no visible binding for global variable 'obsnames'
.PCAplot: no visible global function definition for 'geom_hline'
.PCAplot: no visible global function definition for 'geom_vline'
.PCAplot: no visible global function definition for 'geom_text'
.PCAplot: no visible binding for global variable 'v1'
.PCAplot: no visible binding for global variable 'v2'
.PCAplot: no visible binding for global variable 'varnames'
.PCAplot: no visible global function definition for 'geom_segment'
.PCAplot: no visible global function definition for 'arrow'
.PCAplot: no visible global function definition for 'unit'
.PCAplot: no visible global function definition for 'theme_bw'
.QCTable: no visible global function definition for 'dbGetQuery'
.addFeatures: no visible global function definition for 'make.db.names'
.addFeatures: no visible global function definition for 'dbWriteTable'
.addFeatures: no visible global function definition for 'dbGetQuery'
.as.GRanges: no visible global function definition for 'GRanges'
.as.GRanges: no visible global function definition for 'Rle'
.as.GRanges: no visible global function definition for 'IRanges'
.as.GRanges: no visible global function definition for
'elementMetadata'
.as.GRanges: no visible global function definition for
'elementMetadata<-'
.barplot: no visible global function definition for 'ggplot'
.barplot: no visible global function definition for 'aes'
.barplot: no visible binding for global variable 'sample_name'
.barplot: no visible global function definition for 'geom_bar'
.barplot: no visible global function definition for 'geom_point'
.barplot: no visible global function definition for 'geom_errorbar'
.barplot: no visible binding for global variable 'conf_lo'
.barplot: no visible binding for global variable 'conf_hi'
.barplot: no visible global function definition for 'scale_y_log10'
.barplot: no visible global function definition for 'facet_wrap'
.barplot: no visible global function definition for 'labs'
.barplot: no visible global function definition for 'theme'
.barplot: no visible global function definition for 'element_text'
.barplot: no visible global function definition for 'ylab'
.barplot: no visible global function definition for 'geom_text'
.barplot: no visible binding for global variable 'quant_status'
.barplot: no visible global function definition for 'scale_fill_hue'
.barplot: no visible global function definition for
'scale_colour_manual'
.boxplot: no visible global function definition for 'ggplot'
.boxplot: no visible global function definition for 'geom_boxplot'
.boxplot: no visible global function definition for 'aes'
.boxplot: no visible binding for global variable 'condition'
.boxplot: no visible global function definition for 'theme'
.boxplot: no visible global function definition for 'element_text'
.boxplot: no visible global function definition for 'scale_fill_hue'
.checkReps: no visible global function definition for 'dbReadTable'
.checkSamples: no visible global function definition for 'dbReadTable'
.cluster: no visible global function definition for 'pam'
.confidencePlot: no visible global function definition for 'ggplot'
.confidencePlot: no visible global function definition for 'geom_point'
.confidencePlot: no visible global function definition for 'aes'
.confidencePlot: no visible binding for global variable 'CV'
.confidencePlot: no visible global function definition for
'geom_smooth'
.confidencePlot: no visible binding for global variable 'sample_name'
.confidencePlot: no visible global function definition for
'geom_abline'
.confidencePlot: no visible global function definition for
'scale_color_gradient'
.confidencePlot: no visible global function definition for 'labs'
.countMatrix: no visible global function definition for 'melt'
.countMatrix: no visible global function definition for 'dcast'
.cuff2db: no visible global function definition for 'import'
.cuff2db: no visible global function definition for 'values'
.cuff2db: no visible global function definition for 'seqnames'
.cuff2db: no visible global function definition for 'start'
.cuff2db: no visible global function definition for 'strand'
.cuff2db: no visible global function definition for 'ranges'
.cuff2db: no visible global function definition for 'end'
.cuff2db: no visible global function definition for 'elementNROWS'
.cuff2db: no visible global function definition for 'makeTxDb'
.dendro: no visible global function definition for 'as.dendrogram'
.dendro: no visible global function definition for 'hclust'
.density: no visible global function definition for 'ggplot'
.density: no visible global function definition for 'geom_density'
.density: no visible global function definition for 'aes'
.density: no visible binding for global variable 'condition'
.density: no visible global function definition for 'scale_fill_hue'
.density: no visible global function definition for 'scale_color_hue'
.diffTable: no visible global function definition for 'melt'
.diffTable: no visible global function definition for 'dcast'
.dispersionPlot: no visible global function definition for 'ggplot'
.dispersionPlot: no visible global function definition for 'geom_point'
.dispersionPlot: no visible global function definition for 'aes'
.dispersionPlot: no visible binding for global variable 'dispersion'
.dispersionPlot: no visible binding for global variable 'sample_name'
.dispersionPlot: no visible global function definition for 'facet_wrap'
.dispersionPlot: no visible global function definition for
'scale_x_log10'
.dispersionPlot: no visible global function definition for
'scale_y_log10'
.distheat: no visible global function definition for 'hclust'
.distheat: no visible global function definition for 'melt'
.distheat: no visible global function definition for 'ggplot'
.distheat: no visible global function definition for 'aes'
.distheat: no visible binding for global variable 'X1'
.distheat: no visible binding for global variable 'X2'
.distheat: no visible binding for global variable 'value'
.distheat: no visible global function definition for 'geom_tile'
.distheat: no visible global function definition for 'scale_x_discrete'
.distheat: no visible global function definition for 'scale_y_discrete'
.distheat: no visible global function definition for 'theme'
.distheat: no visible global function definition for 'element_text'
.distheat: no visible global function definition for 'element_line'
.distheat: no visible global function definition for 'element_rect'
.distheat: no visible global function definition for
'scale_fill_gradient'
.distheat: no visible global function definition for
'scale_fill_gradient2'
.distheat: no visible global function definition for 'geom_text'
.expressionPlot: no visible binding for global variable 'mean_cl_boot'
.expressionPlot: no visible global function definition for 'ggplot'
.expressionPlot: no visible global function definition for 'geom_line'
.expressionPlot: no visible global function definition for 'aes'
.expressionPlot: no visible binding for global variable 'sample_name'
.expressionPlot: no visible binding for global variable 'tracking_id'
.expressionPlot: no visible global function definition for 'geom_point'
.expressionPlot: no visible global function definition for
'geom_errorbar'
.expressionPlot: no visible binding for global variable 'conf_lo'
.expressionPlot: no visible binding for global variable 'conf_hi'
.expressionPlot: no visible global function definition for
'scale_y_log10'
.expressionPlot: no visible binding for global variable 'quant_status'
.expressionPlot: no visible global function definition for
'stat_summary'
.expressionPlot: no visible global function definition for 'ylab'
.expressionPlot: no visible global function definition for
'scale_fill_hue'
.expressionPlot: no visible global function definition for
'scale_color_hue'
.expressionPlot: no visible global function definition for 'labs'
.expressionPlot: no visible global function definition for 'theme'
.expressionPlot: no visible global function definition for
'element_text'
.expressionPlot: no visible global function definition for 'facet_wrap'
.fcheatmap: no visible binding for global variable 'dist'
.fcheatmap: no visible global function definition for 'hclust'
.fcheatmap: no visible global function definition for 'melt'
.fcheatmap: no visible global function definition for 'ggplot'
.fcheatmap: no visible global function definition for 'geom_rect'
.fcheatmap: no visible global function definition for 'aes'
.fcheatmap: no visible binding for global variable 'colInd'
.fcheatmap: no visible binding for global variable 'rowInd'
.fcheatmap: no visible binding for global variable 'value'
.fcheatmap: no visible global function definition for
'scale_x_continuous'
.fcheatmap: no visible global function definition for
'scale_y_continuous'
.fcheatmap: no visible global function definition for 'theme'
.fcheatmap: no visible global function definition for 'element_blank'
.fcheatmap: no visible global function definition for 'element_line'
.fcheatmap: no visible global function definition for 'element_rect'
.fcheatmap: no visible global function definition for 'element_text'
.fcheatmap: no visible global function definition for
'scale_fill_gradient'
.fcheatmap: no visible global function definition for
'scale_fill_gradient2'
.findGene: no visible global function definition for 'dbGetQuery'
.findK: no visible global function definition for 'pam'
.fpkmMatrix: no visible global function definition for 'melt'
.fpkmMatrix: no visible global function definition for 'dcast'
.fpkmSCVPlot : <anonymous>: no visible global function definition for
'sd'
.fpkmSCVPlot: no visible global function definition for 'melt'
.fpkmSCVPlot: no visible global function definition for 'ggplot'
.fpkmSCVPlot: no visible global function definition for 'aes'
.fpkmSCVPlot: no visible binding for global variable 'stdev'
.fpkmSCVPlot: no visible global function definition for 'stat_smooth'
.fpkmSCVPlot: no visible binding for global variable 'sample_name'
.fpkmSCVPlot: no visible global function definition for 'scale_x_log10'
.fpkmSCVPlot: no visible global function definition for
'scale_y_continuous'
.fpkmSCVPlot: no visible global function definition for 'xlab'
.fpkmSCVPlot: no visible global function definition for 'theme_bw'
.fpkmSCVPlot: no visible global function definition for 'xlim'
.fpkmSCVPlot: no visible global function definition for 'labs'
.getCountMA: no visible global function definition for 'dbGetQuery'
.getFeatures: no visible global function definition for 'dbSendQuery'
.getFeatures: no visible global function definition for 'dbGetQuery'
.getGene: no visible global function definition for 'dbSendQuery'
.getGene: no visible global function definition for 'dbGetQuery'
.getGeneId: no visible global function definition for 'dbGetQuery'
.getGenes: no visible global function definition for 'dbSendQuery'
.getGenes: no visible global function definition for 'dbGetQuery'
.getGenome: no visible global function definition for 'dbGetQuery'
.getLevels: no visible global function definition for 'dbGetQuery'
.getMA: no visible global function definition for 'dbGetQuery'
.getRepConditionLevels: no visible global function definition for
'dbGetQuery'
.getRepLevels: no visible global function definition for 'dbGetQuery'
.getSig: no visible global function definition for 'dbGetQuery'
.getSig: no visible global function definition for 'p.adjust'
.getSigTable: no visible global function definition for 'dbGetQuery'
.getSigTable: no visible global function definition for 'p.adjust'
.getSigTable: no visible global function definition for 'acast'
.getSigTable: no visible global function definition for 'as.formula'
.ggheat: no visible global function definition for 'hclust'
.ggheat: no visible global function definition for 'melt'
.ggheat: no visible global function definition for 'ggplot'
.ggheat: no visible global function definition for 'geom_rect'
.ggheat: no visible global function definition for 'aes'
.ggheat: no visible binding for global variable 'colInd'
.ggheat: no visible binding for global variable 'rowInd'
.ggheat: no visible binding for global variable 'value'
.ggheat: no visible global function definition for 'scale_x_continuous'
.ggheat: no visible global function definition for 'scale_y_continuous'
.ggheat: no visible global function definition for 'theme'
.ggheat: no visible global function definition for 'element_blank'
.ggheat: no visible global function definition for 'element_line'
.ggheat: no visible global function definition for 'element_rect'
.ggheat: no visible global function definition for 'element_text'
.ggheat: no visible global function definition for
'scale_fill_gradient'
.ggheat: no visible global function definition for
'scale_fill_gradient2'
.hclustToJSON: no visible global function definition for 'toJSON'
.heatmap: no visible global function definition for 'ggplot'
.heatmap: no visible global function definition for 'geom_tile'
.heatmap: no visible global function definition for 'aes'
.heatmap: no visible binding for global variable 'tracking_id'
.heatmap: no visible binding for global variable 'sample_name'
.heatmap: no visible global function definition for
'scale_fill_gradient'
.heatmap: no visible global function definition for 'theme'
.heatmap: no visible global function definition for 'element_text'
.ideogram: no visible global function definition for 'plotIdeogram'
.loadGTF: no visible global function definition for 'import'
.loadGTF: no visible global function definition for 'dbWriteTable'
.makeGRanges: no visible global function definition for 'dbGetQuery'
.makeGRanges: no visible global function definition for 'GRanges'
.makeGRanges: no visible global function definition for 'IRanges'
.makeGeneRegionTrack: no visible global function definition for
'GeneRegionTrack'
.makeRnk: no visible global function definition for 'dbGetQuery'
.makeRnk: no visible global function definition for 'write.table'
.makeRnkTest: no visible global function definition for 'dbGetQuery'
.makeRnkTest: no visible global function definition for 'write.table'
.makeRnkTestStat: no visible global function definition for
'dbGetQuery'
.makeRnkTestStat: no visible global function definition for
'write.table'
.nmf: no visible global function definition for 'nnmf'
.pie: no visible global function definition for 'ggplot'
.pie: no visible global function definition for 'aes'
.pie: no visible binding for global variable 'tracking_id'
.pie: no visible global function definition for 'geom_bar'
.pie: no visible global function definition for 'coord_polar'
.pie: no visible global function definition for 'scale_fill_hue'
.pie: no visible global function definition for 'scale_color_hue'
.pie: no visible global function definition for 'theme_bw'
.pie: no visible global function definition for 'facet_wrap'
.pie: no visible global function definition for 'theme'
.pie: no visible global function definition for 'element_blank'
.plot: no visible global function definition for 'IdeogramTrack'
.plot: no visible global function definition for 'GenomeAxisTrack'
.plot: no visible global function definition for
'BiomartGeneRegionTrack'
.plot: no visible global function definition for 'plotTracks'
.plot2: no visible global function definition for 'theme_bw'
.plot2: no visible global function definition for 'theme'
.plot2: no visible global function definition for 'hasAxis<-'
.plot2: no visible global function definition for 'ggplot'
.plot2: no visible global function definition for 'tracks'
.plotmatrix: no visible global function definition for 'aes'
.plotmatrix: no visible binding for global variable 'x'
.plotmatrix: no visible binding for global variable 'y'
.plotmatrix: no visible global function definition for 'aes_string'
.plotmatrix: no visible global function definition for 'ggplot'
.plotmatrix: no visible global function definition for 'facet_grid'
.plotmatrix: no visible global function definition for 'geom_hex'
.plotmatrix: no visible global function definition for 'geom_point'
.plotmatrix: no visible global function definition for 'stat_density'
.plotmatrix: no visible binding for global variable '..scaled..'
.ratioCluster: no visible global function definition for 'dist'
.ratioCluster: no visible global function definition for 'pam'
.recordGenome: no visible global function definition for 'dbSendQuery'
.repCountMatrix: no visible global function definition for 'melt'
.repCountMatrix: no visible global function definition for 'dcast'
.repFpkmMatrix: no visible global function definition for 'melt'
.repFpkmMatrix: no visible global function definition for 'dcast'
.runInfo: no visible global function definition for 'dbGetQuery'
.scatter: no visible global function definition for 'str_split_fixed'
.scatter: no visible global function definition for 'ggplot'
.scatter: no visible global function definition for 'aes_string'
.scatter: no visible global function definition for 'geom_point'
.scatter: no visible global function definition for 'geom_abline'
.scatter: no visible global function definition for 'geom_rug'
.scatter: no visible global function definition for 'stat_smooth'
.scatter: no visible global function definition for 'geom_text'
.scatter: no visible global function definition for 'scale_y_log10'
.scatter: no visible global function definition for 'scale_x_log10'
.scatter: no visible global function definition for 'ylab'
.scatter: no visible global function definition for 'xlab'
.scatter2: no visible global function definition for 'dbGetQuery'
.scatter2: no visible global function definition for 'ggplot'
.scatter2: no visible global function definition for 'theme_bw'
.scatter2: no visible global function definition for 'aes_string'
.scatter2: no visible global function definition for 'geom_point'
.scatter2: no visible global function definition for 'aes'
.scatter2: no visible binding for global variable 'significant'
.scatter2: no visible global function definition for
'scale_color_manual'
.scatter2: no visible global function definition for 'geom_abline'
.scatter2: no visible global function definition for 'geom_rug'
.scatter2: no visible global function definition for 'stat_smooth'
.scatter2: no visible global function definition for 'geom_text'
.scatter2: no visible global function definition for 'scale_y_log10'
.scatter2: no visible global function definition for 'scale_x_log10'
.scatter2: no visible global function definition for 'labs'
.scatterMat: no visible global function definition for 'geom_abline'
.scatterMat: no visible global function definition for 'theme_bw'
.scatterMat: no visible global function definition for 'ylab'
.scatterMat: no visible global function definition for 'xlab'
.sigMatrix: no visible global function definition for 'dbGetQuery'
.sigMatrix: no visible global function definition for 'p.adjust'
.sigMatrix: no visible global function definition for
'order.dendrogram'
.sigMatrix: no visible global function definition for 'as.dendrogram'
.sigMatrix: no visible global function definition for 'hclust'
.sigMatrix: no visible global function definition for 'ggplot'
.sigMatrix: no visible global function definition for 'aes'
.sigMatrix: no visible binding for global variable 'sample_1'
.sigMatrix: no visible binding for global variable 'sample_2'
.sigMatrix: no visible global function definition for 'stat_sum'
.sigMatrix: no visible binding for global variable '..n..'
.sigMatrix: no visible global function definition for
'scale_fill_continuous'
.sigMatrix: no visible global function definition for 'expand_limits'
.sigMatrix: no visible global function definition for 'theme_bw'
.sigMatrix: no visible global function definition for 'labs'
.sigMatrix: no visible global function definition for 'theme'
.sigMatrix: no visible global function definition for 'element_text'
.sigMatrix: no visible global function definition for 'coord_equal'
.statsMatrix: no visible global function definition for 'dbGetQuery'
.values: no visible global function definition for 'dbGetQuery'
.varModel: no visible global function definition for 'dbGetQuery'
.volcano: no visible global function definition for 'ggplot'
.volcano: no visible global function definition for 'geom_point'
.volcano: no visible global function definition for 'aes'
.volcano: no visible binding for global variable 'log2_fold_change'
.volcano: no visible binding for global variable 'p_value'
.volcano: no visible binding for global variable 'significant'
.volcano: no visible global function definition for 'labs'
.volcano: no visible global function definition for
'scale_x_continuous'
.volcano: no visible global function definition for
'scale_colour_manual'
.volcanoMatrix: no visible global function definition for 'aes'
.volcanoMatrix: no visible global function definition for 'aes_string'
.volcanoMatrix: no visible global function definition for 'ggplot'
.volcanoMatrix: no visible global function definition for 'geom_point'
.volcanoMatrix: no visible global function definition for
'scale_colour_manual'
.volcanoMatrix: no visible global function definition for 'facet_grid'
.volcanoMatrix: no visible global function definition for 'geom_vline'
.volcanoMatrix: no visible global function definition for 'theme_bw'
.volcanoMatrix: no visible global function definition for 'xlab'
.volcanoMatrix: no visible global function definition for 'ylab'
JSdist: no visible global function definition for 'as.dist'
bulk_insert: no visible global function definition for 'dbBegin'
bulk_insert: no visible global function definition for
'dbGetPreparedQuery'
bulk_insert: no visible global function definition for 'dbCommit'
createDB_noIndex: no visible global function definition for 'dbDriver'
createDB_noIndex: no visible global function definition for 'dbConnect'
createDB_noIndex : <anonymous>: no visible global function definition
for 'dbGetQuery'
createIndices: no visible global function definition for 'dbDriver'
createIndices: no visible global function definition for 'dbConnect'
createIndices : <anonymous>: no visible global function definition for
'dbGetQuery'
csClusterPlot: no visible binding for global variable 'mean_cl_boot'
csClusterPlot: no visible global function definition for 'melt'
csClusterPlot: no visible global function definition for 'ggplot'
csClusterPlot: no visible global function definition for 'geom_line'
csClusterPlot: no visible global function definition for 'aes'
csClusterPlot: no visible binding for global variable 'variable'
csClusterPlot: no visible binding for global variable 'value'
csClusterPlot: no visible binding for global variable 'cluster'
csClusterPlot: no visible binding for global variable 'ids'
csClusterPlot: no visible global function definition for 'theme_bw'
csClusterPlot: no visible global function definition for 'facet_wrap'
csClusterPlot: no visible global function definition for 'stat_summary'
csClusterPlot: no visible global function definition for
'scale_y_log10'
csClusterPlot: no visible global function definition for
'scale_color_hue'
csClusterPlot: no visible global function definition for 'theme'
csClusterPlot: no visible global function definition for 'element_text'
expressionPlot: no visible binding for global variable 'mean_cl_boot'
loadCDS: no visible binding for global variable 'read.table'
loadCDS: no visible global function definition for 'make.db.names'
loadCDS: no visible global function definition for 'dbReadTable'
loadCDS: no visible global function definition for 'melt'
loadCDS: no visible global function definition for 'dcast'
loadGenes: no visible binding for global variable 'read.table'
loadGenes: no visible global function definition for 'make.db.names'
loadGenes: no visible global function definition for 'dbReadTable'
loadGenes: no visible global function definition for 'melt'
loadGenes: no visible global function definition for 'dcast'
loadIsoforms: no visible binding for global variable 'read.table'
loadIsoforms: no visible global function definition for 'make.db.names'
loadIsoforms: no visible global function definition for 'dbReadTable'
loadIsoforms: no visible global function definition for 'melt'
loadIsoforms: no visible global function definition for 'dcast'
loadRepTable: no visible global function definition for 'read.delim'
loadRepTable: no visible global function definition for 'make.db.names'
loadRunInfo: no visible binding for global variable 'read.table'
loadTSS: no visible binding for global variable 'read.table'
loadTSS: no visible global function definition for 'make.db.names'
loadTSS: no visible global function definition for 'dbReadTable'
loadTSS: no visible global function definition for 'melt'
loadTSS: no visible global function definition for 'dcast'
loadVarModelTable: no visible global function definition for
'read.delim'
loadVarModelTable: no visible global function definition for
'make.db.names'
populateSampleTable: no visible global function definition for
'make.db.names'
populateSampleTable: no visible global function definition for
'dbWriteTable'
readCufflinks: no visible global function definition for 'dbConnect'
readCufflinks: no visible global function definition for 'dbDriver'
MAplot,CuffData: no visible global function definition for 'ggplot'
MAplot,CuffData: no visible global function definition for 'geom_point'
MAplot,CuffData: no visible global function definition for 'aes'
MAplot,CuffData: no visible binding for global variable 'A'
MAplot,CuffData: no visible binding for global variable 'M'
MAplot,CuffData: no visible global function definition for
'stat_smooth'
MAplot,CuffData: no visible global function definition for 'geom_hline'
MDSplot,CuffData: no visible global function definition for 'cmdscale'
MDSplot,CuffData: no visible global function definition for 'ggplot'
MDSplot,CuffData: no visible global function definition for
'geom_point'
MDSplot,CuffData: no visible global function definition for 'aes'
MDSplot,CuffData: no visible binding for global variable 'M1'
MDSplot,CuffData: no visible binding for global variable 'M2'
MDSplot,CuffData: no visible global function definition for 'geom_text'
MDSplot,CuffData: no visible global function definition for 'theme_bw'
MDSplot,CuffFeatureSet: no visible global function definition for
'cmdscale'
MDSplot,CuffFeatureSet: no visible global function definition for
'ggplot'
MDSplot,CuffFeatureSet: no visible global function definition for
'geom_point'
MDSplot,CuffFeatureSet: no visible global function definition for 'aes'
MDSplot,CuffFeatureSet: no visible binding for global variable 'M1'
MDSplot,CuffFeatureSet: no visible binding for global variable 'M2'
MDSplot,CuffFeatureSet: no visible global function definition for
'geom_text'
MDSplot,CuffFeatureSet: no visible global function definition for
'theme_bw'
PCAplot,CuffData: no visible global function definition for 'prcomp'
PCAplot,CuffData: no visible global function definition for 'ggplot'
PCAplot,CuffData: no visible global function definition for
'aes_string'
PCAplot,CuffData: no visible global function definition for
'geom_point'
PCAplot,CuffData: no visible global function definition for 'aes'
PCAplot,CuffData: no visible binding for global variable 'obsnames'
PCAplot,CuffData: no visible global function definition for
'geom_hline'
PCAplot,CuffData: no visible global function definition for
'geom_vline'
PCAplot,CuffData: no visible global function definition for 'geom_text'
PCAplot,CuffData: no visible binding for global variable 'v1'
PCAplot,CuffData: no visible binding for global variable 'v2'
PCAplot,CuffData: no visible binding for global variable 'varnames'
PCAplot,CuffData: no visible global function definition for
'geom_segment'
PCAplot,CuffData: no visible global function definition for 'arrow'
PCAplot,CuffData: no visible global function definition for 'unit'
PCAplot,CuffData: no visible global function definition for 'theme_bw'
PCAplot,CuffFeatureSet: no visible global function definition for
'prcomp'
PCAplot,CuffFeatureSet: no visible global function definition for
'ggplot'
PCAplot,CuffFeatureSet: no visible global function definition for
'aes_string'
PCAplot,CuffFeatureSet: no visible global function definition for
'geom_point'
PCAplot,CuffFeatureSet: no visible global function definition for 'aes'
PCAplot,CuffFeatureSet: no visible binding for global variable
'obsnames'
PCAplot,CuffFeatureSet: no visible global function definition for
'geom_hline'
PCAplot,CuffFeatureSet: no visible global function definition for
'geom_vline'
PCAplot,CuffFeatureSet: no visible global function definition for
'geom_text'
PCAplot,CuffFeatureSet: no visible binding for global variable 'v1'
PCAplot,CuffFeatureSet: no visible binding for global variable 'v2'
PCAplot,CuffFeatureSet: no visible binding for global variable
'varnames'
PCAplot,CuffFeatureSet: no visible global function definition for
'geom_segment'
PCAplot,CuffFeatureSet: no visible global function definition for
'arrow'
PCAplot,CuffFeatureSet: no visible global function definition for
'unit'
PCAplot,CuffFeatureSet: no visible global function definition for
'theme_bw'
addFeatures,CuffData: no visible global function definition for
'make.db.names'
addFeatures,CuffData: no visible global function definition for
'dbWriteTable'
addFeatures,CuffData: no visible global function definition for
'dbGetQuery'
addFeatures,CuffSet: no visible global function definition for
'make.db.names'
addFeatures,CuffSet: no visible global function definition for
'dbWriteTable'
addFeatures,CuffSet: no visible global function definition for
'dbGetQuery'
annotation,CuffData: no visible global function definition for
'dbGetQuery'
coerce,CuffGene-GRanges: no visible global function definition for
'GRanges'
coerce,CuffGene-GRanges: no visible global function definition for
'Rle'
coerce,CuffGene-GRanges: no visible global function definition for
'IRanges'
coerce,CuffGene-GRanges: no visible global function definition for
'elementMetadata'
coerce,CuffGene-GRanges: no visible global function definition for
'elementMetadata<-'
count,CuffData: no visible global function definition for 'dbGetQuery'
countMatrix,CuffData: no visible global function definition for
'dbGetQuery'
countMatrix,CuffFeatureSet: no visible global function definition for
'melt'
countMatrix,CuffFeatureSet: no visible global function definition for
'dcast'
csBoxplot,CuffData: no visible global function definition for 'ggplot'
csBoxplot,CuffData: no visible global function definition for
'geom_boxplot'
csBoxplot,CuffData: no visible global function definition for 'aes'
csBoxplot,CuffData: no visible binding for global variable 'condition'
csBoxplot,CuffData: no visible global function definition for 'theme'
csBoxplot,CuffData: no visible global function definition for
'element_text'
csBoxplot,CuffData: no visible global function definition for
'scale_fill_hue'
csCluster,CuffFeatureSet: no visible global function definition for
'pam'
csDendro,CuffData: no visible global function definition for
'as.dendrogram'
csDendro,CuffData: no visible global function definition for 'hclust'
csDendro,CuffFeatureSet: no visible global function definition for
'as.dendrogram'
csDendro,CuffFeatureSet: no visible global function definition for
'hclust'
csDensity,CuffData: no visible global function definition for 'ggplot'
csDensity,CuffData: no visible global function definition for
'geom_density'
csDensity,CuffData: no visible global function definition for 'aes'
csDensity,CuffData: no visible binding for global variable 'condition'
csDensity,CuffData: no visible global function definition for 'labs'
csDensity,CuffData: no visible global function definition for
'scale_fill_hue'
csDensity,CuffData: no visible global function definition for
'scale_color_hue'
csDensity,CuffFeatureSet: no visible global function definition for
'ggplot'
csDensity,CuffFeatureSet: no visible global function definition for
'geom_density'
csDensity,CuffFeatureSet: no visible global function definition for
'aes'
csDensity,CuffFeatureSet: no visible binding for global variable
'condition'
csDensity,CuffFeatureSet: no visible global function definition for
'scale_fill_hue'
csDensity,CuffFeatureSet: no visible global function definition for
'scale_color_hue'
csDistHeat,CuffData: no visible global function definition for 'hclust'
csDistHeat,CuffData: no visible global function definition for 'melt'
csDistHeat,CuffData: no visible global function definition for 'ggplot'
csDistHeat,CuffData: no visible global function definition for 'aes'
csDistHeat,CuffData: no visible binding for global variable 'X1'
csDistHeat,CuffData: no visible binding for global variable 'X2'
csDistHeat,CuffData: no visible binding for global variable 'value'
csDistHeat,CuffData: no visible global function definition for
'geom_tile'
csDistHeat,CuffData: no visible global function definition for
'scale_x_discrete'
csDistHeat,CuffData: no visible global function definition for
'scale_y_discrete'
csDistHeat,CuffData: no visible global function definition for 'theme'
csDistHeat,CuffData: no visible global function definition for
'element_text'
csDistHeat,CuffData: no visible global function definition for
'element_line'
csDistHeat,CuffData: no visible global function definition for
'element_rect'
csDistHeat,CuffData: no visible global function definition for
'scale_fill_gradient'
csDistHeat,CuffData: no visible global function definition for
'scale_fill_gradient2'
csDistHeat,CuffData: no visible global function definition for
'geom_text'
csDistHeat,CuffFeatureSet: no visible global function definition for
'hclust'
csDistHeat,CuffFeatureSet: no visible global function definition for
'melt'
csDistHeat,CuffFeatureSet: no visible global function definition for
'ggplot'
csDistHeat,CuffFeatureSet: no visible global function definition for
'aes'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X1'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X2'
csDistHeat,CuffFeatureSet: no visible binding for global variable
'value'
csDistHeat,CuffFeatureSet: no visible global function definition for
'geom_tile'
csDistHeat,CuffFeatureSet: no visible global function definition for
'scale_x_discrete'
csDistHeat,CuffFeatureSet: no visible global function definition for
'scale_y_discrete'
csDistHeat,CuffFeatureSet: no visible global function definition for
'theme'
csDistHeat,CuffFeatureSet: no visible global function definition for
'element_text'
csDistHeat,CuffFeatureSet: no visible global function definition for
'element_line'
csDistHeat,CuffFeatureSet: no visible global function definition for
'element_rect'
csDistHeat,CuffFeatureSet: no visible global function definition for
'scale_fill_gradient'
csDistHeat,CuffFeatureSet: no visible global function definition for
'scale_fill_gradient2'
csDistHeat,CuffFeatureSet: no visible global function definition for
'geom_text'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
variable 'dist'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'hclust'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'melt'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'ggplot'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'geom_rect'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'aes'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
variable 'colInd'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
variable 'rowInd'
csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global
variable 'value'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'scale_x_continuous'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'scale_y_continuous'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'theme'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'element_blank'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'element_line'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'element_rect'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'element_text'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'scale_fill_gradient'
csFoldChangeHeatmap,CuffFeatureSet: no visible global function
definition for 'scale_fill_gradient2'
csHeatmap,CuffFeatureSet: no visible global function definition for
'hclust'
csHeatmap,CuffFeatureSet: no visible global function definition for
'melt'
csHeatmap,CuffFeatureSet: no visible global function definition for
'ggplot'
csHeatmap,CuffFeatureSet: no visible global function definition for
'geom_rect'
csHeatmap,CuffFeatureSet: no visible global function definition for
'aes'
csHeatmap,CuffFeatureSet: no visible binding for global variable
'colInd'
csHeatmap,CuffFeatureSet: no visible binding for global variable
'rowInd'
csHeatmap,CuffFeatureSet: no visible binding for global variable
'value'
csHeatmap,CuffFeatureSet: no visible global function definition for
'scale_x_continuous'
csHeatmap,CuffFeatureSet: no visible global function definition for
'scale_y_continuous'
csHeatmap,CuffFeatureSet: no visible global function definition for
'theme'
csHeatmap,CuffFeatureSet: no visible global function definition for
'element_blank'
csHeatmap,CuffFeatureSet: no visible global function definition for
'element_line'
csHeatmap,CuffFeatureSet: no visible global function definition for
'element_rect'
csHeatmap,CuffFeatureSet: no visible global function definition for
'element_text'
csHeatmap,CuffFeatureSet: no visible global function definition for
'scale_fill_gradient'
csHeatmap,CuffFeatureSet: no visible global function definition for
'scale_fill_gradient2'
csNMF,CuffData: no visible global function definition for 'nnmf'
csNMF,CuffFeatureSet: no visible global function definition for 'nnmf'
csPie,CuffGene: no visible global function definition for 'ggplot'
csPie,CuffGene: no visible global function definition for 'aes'
csPie,CuffGene: no visible binding for global variable 'tracking_id'
csPie,CuffGene: no visible global function definition for 'geom_bar'
csPie,CuffGene: no visible global function definition for 'coord_polar'
csPie,CuffGene: no visible global function definition for
'scale_fill_hue'
csPie,CuffGene: no visible global function definition for
'scale_color_hue'
csPie,CuffGene: no visible global function definition for 'theme_bw'
csPie,CuffGene: no visible global function definition for 'facet_wrap'
csPie,CuffGene: no visible global function definition for 'theme'
csPie,CuffGene: no visible global function definition for
'element_blank'
csScatter,CuffData: no visible global function definition for
'str_split_fixed'
csScatter,CuffData: no visible global function definition for 'ggplot'
csScatter,CuffData: no visible global function definition for
'aes_string'
csScatter,CuffData: no visible global function definition for
'geom_point'
csScatter,CuffData: no visible global function definition for
'geom_abline'
csScatter,CuffData: no visible global function definition for
'geom_rug'
csScatter,CuffData: no visible global function definition for
'stat_smooth'
csScatter,CuffData: no visible global function definition for
'geom_text'
csScatter,CuffData: no visible global function definition for
'scale_y_log10'
csScatter,CuffData: no visible global function definition for
'scale_x_log10'
csScatter,CuffData: no visible global function definition for 'labs'
csScatter,CuffFeatureSet: no visible global function definition for
'str_split_fixed'
csScatter,CuffFeatureSet: no visible global function definition for
'ggplot'
csScatter,CuffFeatureSet: no visible global function definition for
'aes_string'
csScatter,CuffFeatureSet: no visible global function definition for
'geom_point'
csScatter,CuffFeatureSet: no visible global function definition for
'geom_abline'
csScatter,CuffFeatureSet: no visible global function definition for
'geom_rug'
csScatter,CuffFeatureSet: no visible global function definition for
'stat_smooth'
csScatter,CuffFeatureSet: no visible global function definition for
'geom_text'
csScatter,CuffFeatureSet: no visible global function definition for
'scale_y_log10'
csScatter,CuffFeatureSet: no visible global function definition for
'scale_x_log10'
csScatter,CuffFeatureSet: no visible global function definition for
'ylab'
csScatter,CuffFeatureSet: no visible global function definition for
'xlab'
csScatterMatrix,CuffData: no visible global function definition for
'geom_abline'
csScatterMatrix,CuffData: no visible global function definition for
'theme_bw'
csScatterMatrix,CuffData: no visible global function definition for
'ylab'
csScatterMatrix,CuffData: no visible global function definition for
'xlab'
csVolcano,CuffData: no visible global function definition for 'ggplot'
csVolcano,CuffData: no visible global function definition for
'geom_point'
csVolcano,CuffData: no visible global function definition for 'aes'
csVolcano,CuffData: no visible binding for global variable
'log2_fold_change'
csVolcano,CuffData: no visible binding for global variable 'p_value'
csVolcano,CuffData: no visible binding for global variable
'significant'
csVolcano,CuffData: no visible global function definition for
'theme_bw'
csVolcano,CuffData: no visible global function definition for 'labs'
csVolcano,CuffData: no visible global function definition for
'scale_colour_manual'
csVolcano,CuffData: no visible global function definition for
'scale_x_continuous'
csVolcano,CuffData: no visible global function definition for 'xlab'
csVolcano,CuffData: no visible global function definition for 'ylab'
csVolcano,CuffFeatureSet: no visible global function definition for
'ggplot'
csVolcano,CuffFeatureSet: no visible global function definition for
'geom_point'
csVolcano,CuffFeatureSet: no visible global function definition for
'aes'
csVolcano,CuffFeatureSet: no visible binding for global variable
'log2_fold_change'
csVolcano,CuffFeatureSet: no visible binding for global variable
'p_value'
csVolcano,CuffFeatureSet: no visible binding for global variable
'significant'
csVolcano,CuffFeatureSet: no visible global function definition for
'labs'
csVolcano,CuffFeatureSet: no visible global function definition for
'scale_x_continuous'
csVolcano,CuffFeatureSet: no visible global function definition for
'scale_colour_manual'
csVolcanoMatrix,CuffData: no visible global function definition for
'aes'
csVolcanoMatrix,CuffData: no visible global function definition for
'aes_string'
csVolcanoMatrix,CuffData: no visible global function definition for
'ggplot'
csVolcanoMatrix,CuffData: no visible global function definition for
'geom_point'
csVolcanoMatrix,CuffData: no visible global function definition for
'scale_colour_manual'
csVolcanoMatrix,CuffData: no visible global function definition for
'facet_grid'
csVolcanoMatrix,CuffData: no visible global function definition for
'geom_vline'
csVolcanoMatrix,CuffData: no visible global function definition for
'theme_bw'
csVolcanoMatrix,CuffData: no visible global function definition for
'xlab'
csVolcanoMatrix,CuffData: no visible global function definition for
'ylab'
diffData,CuffData: no visible global function definition for
'dbGetQuery'
diffTable,CuffData: no visible global function definition for 'melt'
diffTable,CuffData: no visible global function definition for 'dcast'
diffTable,CuffFeatureSet: no visible global function definition for
'melt'
diffTable,CuffFeatureSet: no visible global function definition for
'dcast'
dim,CuffData: no visible global function definition for 'dbGetQuery'
dim,CuffDist: no visible global function definition for 'dbGetQuery'
dispersionPlot,CuffData: no visible global function definition for
'ggplot'
dispersionPlot,CuffData: no visible global function definition for
'geom_point'
dispersionPlot,CuffData: no visible global function definition for
'aes'
dispersionPlot,CuffData: no visible binding for global variable
'dispersion'
dispersionPlot,CuffData: no visible binding for global variable
'sample_name'
dispersionPlot,CuffData: no visible global function definition for
'facet_wrap'
dispersionPlot,CuffData: no visible global function definition for
'scale_x_log10'
dispersionPlot,CuffData: no visible global function definition for
'scale_y_log10'
dispersionPlot,CuffSet: no visible global function definition for
'ggplot'
dispersionPlot,CuffSet: no visible global function definition for
'geom_point'
dispersionPlot,CuffSet: no visible global function definition for 'aes'
dispersionPlot,CuffSet: no visible binding for global variable
'compatible_count_mean'
dispersionPlot,CuffSet: no visible binding for global variable
'compatible_count_var'
dispersionPlot,CuffSet: no visible binding for global variable
'condition'
dispersionPlot,CuffSet: no visible global function definition for
'geom_line'
dispersionPlot,CuffSet: no visible binding for global variable
'fitted_var'
dispersionPlot,CuffSet: no visible global function definition for
'facet_wrap'
dispersionPlot,CuffSet: no visible global function definition for
'scale_y_log10'
dispersionPlot,CuffSet: no visible global function definition for
'scale_x_log10'
dispersionPlot,CuffSet: no visible global function definition for
'theme_bw'
dispersionPlot,CuffSet: no visible global function definition for
'guides'
distValues,CuffDist: no visible global function definition for
'dbGetQuery'
expressionBarplot,CuffFeature: no visible global function definition
for 'ggplot'
expressionBarplot,CuffFeature: no visible global function definition
for 'aes'
expressionBarplot,CuffFeature: no visible binding for global variable
'sample_name'
expressionBarplot,CuffFeature: no visible global function definition
for 'geom_bar'
expressionBarplot,CuffFeature: no visible global function definition
for 'geom_point'
expressionBarplot,CuffFeature: no visible global function definition
for 'geom_errorbar'
expressionBarplot,CuffFeature: no visible binding for global variable
'conf_lo'
expressionBarplot,CuffFeature: no visible binding for global variable
'conf_hi'
expressionBarplot,CuffFeature: no visible global function definition
for 'scale_y_log10'
expressionBarplot,CuffFeature: no visible global function definition
for 'facet_wrap'
expressionBarplot,CuffFeature: no visible global function definition
for 'labs'
expressionBarplot,CuffFeature: no visible global function definition
for 'theme'
expressionBarplot,CuffFeature: no visible global function definition
for 'element_text'
expressionBarplot,CuffFeature: no visible global function definition
for 'ylab'
expressionBarplot,CuffFeature: no visible global function definition
for 'geom_text'
expressionBarplot,CuffFeature: no visible binding for global variable
'quant_status'
expressionBarplot,CuffFeature: no visible global function definition
for 'scale_fill_hue'
expressionBarplot,CuffFeature: no visible global function definition
for 'scale_colour_manual'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'position_dodge'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'ggplot'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'aes'
expressionBarplot,CuffFeatureSet: no visible binding for global
variable 'tracking_id'
expressionBarplot,CuffFeatureSet: no visible binding for global
variable 'sample_name'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'geom_bar'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'geom_errorbar'
expressionBarplot,CuffFeatureSet: no visible binding for global
variable 'conf_lo'
expressionBarplot,CuffFeatureSet: no visible binding for global
variable 'conf_hi'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'scale_y_log10'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'geom_text'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'scale_x_discrete'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'theme'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'element_text'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'ylab'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'scale_fill_hue'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'scale_color_hue'
expressionBarplot,CuffFeatureSet: no visible global function definition
for 'scale_colour_manual'
expressionPlot,CuffFeature: no visible binding for global variable
'mean_cl_boot'
expressionPlot,CuffFeature: no visible global function definition for
'ggplot'
expressionPlot,CuffFeature: no visible global function definition for
'geom_line'
expressionPlot,CuffFeature: no visible global function definition for
'aes'
expressionPlot,CuffFeature: no visible binding for global variable
'sample_name'
expressionPlot,CuffFeature: no visible binding for global variable
'tracking_id'
expressionPlot,CuffFeature: no visible global function definition for
'geom_point'
expressionPlot,CuffFeature: no visible global function definition for
'geom_errorbar'
expressionPlot,CuffFeature: no visible binding for global variable
'conf_lo'
expressionPlot,CuffFeature: no visible binding for global variable
'conf_hi'
expressionPlot,CuffFeature: no visible global function definition for
'scale_y_log10'
expressionPlot,CuffFeature: no visible binding for global variable
'quant_status'
expressionPlot,CuffFeature: no visible global function definition for
'stat_summary'
expressionPlot,CuffFeature: no visible global function definition for
'ylab'
expressionPlot,CuffFeature: no visible global function definition for
'scale_fill_hue'
expressionPlot,CuffFeature: no visible global function definition for
'scale_color_hue'
expressionPlot,CuffFeature: no visible global function definition for
'labs'
expressionPlot,CuffFeature: no visible global function definition for
'theme'
expressionPlot,CuffFeature: no visible global function definition for
'element_text'
expressionPlot,CuffFeature: no visible global function definition for
'facet_wrap'
expressionPlot,CuffFeatureSet: no visible binding for global variable
'mean_cl_boot'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'ggplot'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'geom_line'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'aes'
expressionPlot,CuffFeatureSet: no visible binding for global variable
'sample_name'
expressionPlot,CuffFeatureSet: no visible binding for global variable
'tracking_id'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'geom_point'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'geom_errorbar'
expressionPlot,CuffFeatureSet: no visible binding for global variable
'conf_lo'
expressionPlot,CuffFeatureSet: no visible binding for global variable
'conf_hi'
expressionPlot,CuffFeatureSet: no visible binding for global variable
'quant_status'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'scale_y_log10'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'stat_summary'
expressionPlot,CuffFeatureSet: no visible global function definition
for 'ylab'
featureNames,CuffData: no visible global function definition for
'dbGetQuery'
findGene,CuffSet: no visible global function definition for
'dbGetQuery'
fpkm,CuffData: no visible global function definition for 'dbGetQuery'
fpkmMatrix,CuffData: no visible global function definition for
'dbGetQuery'
fpkmMatrix,CuffFeature: no visible global function definition for
'melt'
fpkmMatrix,CuffFeature: no visible global function definition for
'dcast'
fpkmMatrix,CuffFeatureSet: no visible global function definition for
'melt'
fpkmMatrix,CuffFeatureSet: no visible global function definition for
'dcast'
fpkmSCVPlot,CuffData : <anonymous>: no visible global function
definition for 'sd'
fpkmSCVPlot,CuffData: no visible global function definition for 'melt'
fpkmSCVPlot,CuffData: no visible global function definition for
'ggplot'
fpkmSCVPlot,CuffData: no visible global function definition for 'aes'
fpkmSCVPlot,CuffData: no visible binding for global variable 'stdev'
fpkmSCVPlot,CuffData: no visible global function definition for
'stat_smooth'
fpkmSCVPlot,CuffData: no visible binding for global variable
'sample_name'
fpkmSCVPlot,CuffData: no visible global function definition for
'scale_x_log10'
fpkmSCVPlot,CuffData: no visible global function definition for
'scale_y_continuous'
fpkmSCVPlot,CuffData: no visible global function definition for 'xlab'
fpkmSCVPlot,CuffData: no visible global function definition for
'theme_bw'
fpkmSCVPlot,CuffData: no visible global function definition for 'xlim'
fpkmSCVPlot,CuffData: no visible global function definition for 'labs'
genePlot,CuffGene: no visible global function definition for
'IdeogramTrack'
genePlot,CuffGene: no visible global function definition for
'GenomeAxisTrack'
genePlot,CuffGene: no visible global function definition for
'BiomartGeneRegionTrack'
genePlot,CuffGene: no visible global function definition for
'plotTracks'
getFeatures,CuffSet: no visible global function definition for
'dbSendQuery'
getFeatures,CuffSet: no visible global function definition for
'dbGetQuery'
getGene,CuffSet: no visible global function definition for
'dbSendQuery'
getGene,CuffSet: no visible global function definition for 'dbGetQuery'
getGeneId,CuffSet: no visible global function definition for
'dbGetQuery'
getGenes,CuffSet: no visible global function definition for
'dbSendQuery'
getGenes,CuffSet: no visible global function definition for
'dbGetQuery'
getLevels,CuffData: no visible global function definition for
'dbGetQuery'
getLevels,CuffSet: no visible global function definition for
'dbGetQuery'
getRepLevels,CuffData: no visible global function definition for
'dbGetQuery'
getRepLevels,CuffSet: no visible global function definition for
'dbGetQuery'
getSig,CuffSet: no visible global function definition for 'dbGetQuery'
getSig,CuffSet: no visible global function definition for 'p.adjust'
getSigTable,CuffSet: no visible global function definition for
'dbGetQuery'
getSigTable,CuffSet: no visible global function definition for
'p.adjust'
getSigTable,CuffSet: no visible global function definition for 'acast'
getSigTable,CuffSet: no visible global function definition for
'as.formula'
makeGRanges,CuffSet: no visible global function definition for
'dbGetQuery'
makeGRanges,CuffSet: no visible global function definition for
'GRanges'
makeGRanges,CuffSet: no visible global function definition for
'IRanges'
makeGeneRegionTrack,CuffGene: no visible global function definition for
'GeneRegionTrack'
makeRnk,CuffData: no visible global function definition for
'dbGetQuery'
makeRnk,CuffData: no visible global function definition for
'write.table'
repCountMatrix,CuffData: no visible global function definition for
'dbGetQuery'
repCountMatrix,CuffFeatureSet: no visible global function definition
for 'melt'
repCountMatrix,CuffFeatureSet: no visible global function definition
for 'dcast'
repFpkm,CuffData: no visible global function definition for
'dbGetQuery'
repFpkmMatrix,CuffData: no visible global function definition for
'dbGetQuery'
repFpkmMatrix,CuffFeature: no visible global function definition for
'melt'
repFpkmMatrix,CuffFeature: no visible global function definition for
'dcast'
repFpkmMatrix,CuffFeatureSet: no visible global function definition for
'melt'
repFpkmMatrix,CuffFeatureSet: no visible global function definition for
'dcast'
replicates,CuffData: no visible global function definition for
'dbReadTable'
replicates,CuffSet: no visible global function definition for
'dbGetQuery'
runInfo,CuffSet: no visible global function definition for 'dbGetQuery'
samples,CuffData: no visible global function definition for
'dbReadTable'
samples,CuffDist: no visible global function definition for
'dbReadTable'
samples,CuffSet: no visible global function definition for 'dbGetQuery'
sigMatrix,CuffSet: no visible global function definition for
'dbGetQuery'
sigMatrix,CuffSet: no visible global function definition for 'p.adjust'
sigMatrix,CuffSet: no visible global function definition for
'order.dendrogram'
sigMatrix,CuffSet: no visible global function definition for
'as.dendrogram'
sigMatrix,CuffSet: no visible global function definition for 'hclust'
sigMatrix,CuffSet: no visible global function definition for 'ggplot'
sigMatrix,CuffSet: no visible global function definition for 'aes'
sigMatrix,CuffSet: no visible binding for global variable 'sample_1'
sigMatrix,CuffSet: no visible binding for global variable 'sample_2'
sigMatrix,CuffSet: no visible global function definition for 'stat_sum'
sigMatrix,CuffSet: no visible binding for global variable '..n..'
sigMatrix,CuffSet: no visible global function definition for
'scale_fill_continuous'
sigMatrix,CuffSet: no visible global function definition for
'expand_limits'
sigMatrix,CuffSet: no visible global function definition for 'theme_bw'
sigMatrix,CuffSet: no visible global function definition for 'labs'
sigMatrix,CuffSet: no visible global function definition for 'theme'
sigMatrix,CuffSet: no visible global function definition for
'element_text'
sigMatrix,CuffSet: no visible global function definition for
'coord_equal'
varModel,CuffSet: no visible global function definition for
'dbGetQuery'
Undefined global functions or variables:
..n.. ..scaled.. A BiomartGeneRegionTrack CV GRanges GeneRegionTrack
GenomeAxisTrack IRanges IdeogramTrack M M1 M2 Rle X1 X2 acast aes
aes_string arrow as.dendrogram as.dist as.formula cluster cmdscale
colInd compatible_count_mean compatible_count_var condition conf_hi
conf_lo coord_equal coord_polar dbBegin dbCommit dbConnect dbDriver
dbGetPreparedQuery dbGetQuery dbReadTable dbSendQuery dbWriteTable
dcast dispersion dist elementMetadata elementMetadata<- elementNROWS
element_blank element_line element_rect element_text end
expand_limits facet_grid facet_wrap fitted_var geom_abline geom_bar
geom_boxplot geom_density geom_errorbar geom_hex geom_hline geom_line
geom_point geom_rect geom_rug geom_segment geom_smooth geom_text
geom_tile geom_vline ggplot guides hasAxis<- hclust ids import labs
log2_fold_change make.db.names makeTxDb mean_cl_boot melt nnmf
obsnames order.dendrogram p.adjust p_value pam plotIdeogram
plotTracks position_dodge prcomp quant_status ranges read.delim
read.table rowInd sample_1 sample_2 sample_name scale_color_gradient
scale_color_hue scale_color_manual scale_colour_manual
scale_fill_continuous scale_fill_gradient scale_fill_gradient2
scale_fill_hue scale_x_continuous scale_x_discrete scale_x_log10
scale_y_continuous scale_y_discrete scale_y_log10 sd seqnames
significant start stat_density stat_smooth stat_sum stat_summary
stdev str_split_fixed strand theme theme_bw toJSON tracking_id tracks
unit v1 v2 value values variable varnames write.table x xlab xlim y
ylab
Consider adding
importFrom("stats", "as.dendrogram", "as.dist", "as.formula",
"cmdscale", "dist", "end", "hclust", "order.dendrogram",
"p.adjust", "prcomp", "sd", "start")
importFrom("utils", "read.delim", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'diffData':
‘...’
Documented arguments not in \usage in documentation object 'distValues':
‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘cummeRbund-example-workflow.Rnw’... OK
‘cummeRbund-manual.Rnw’... OK
OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘cummeRbund-example-workflow.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated,
aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit,
which.max, which.min
Loading required package: RSQLite
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: 'cummeRbund'
The following object is masked from 'package:GenomicRanges':
promoters
The following object is masked from 'package:IRanges':
promoters
The following object is masked from 'package:BiocGenerics':
conditions
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Getting gene information:
FPKM
Warning: Closing open result set, pending rows
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting isoforms information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting CDS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting TSS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting promoter information:
distData
Warning: Closing open result set, pending rows
Getting splicing information:
distData
Getting relCDS information:
distData
Warning: Closing open result set, pending rows
Warning: Closing open result set, pending rows
--- finished re-building 'cummeRbund-example-workflow.Rnw'
--- re-building ‘cummeRbund-manual.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated,
aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit,
which.max, which.min
Loading required package: RSQLite
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: 'cummeRbund'
The following object is masked from 'package:GenomicRanges':
promoters
The following object is masked from 'package:IRanges':
promoters
The following object is masked from 'package:BiocGenerics':
conditions
Creating database /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/cuffData.db
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading Run Info File /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/run.info
Writing runInfo Table
Warning: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading Read Group Info /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/read_groups.info
Warning: RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier().
Writing replicates Table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading GTF file
Writing GTF features to 'features' table...
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/genes.fpkm_tracking
Checking samples table...
Warning: Closing open result set, pending rows
Populating samples table...
Writing genes table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reshaping geneData table
Recasting
Writing geneData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/gene_exp.diff
Writing geneExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/promoters.diff
Writing promoterDiffData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading read group info in /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/genes.read_group_tracking
Writing geneReplicateData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reshaping isoformData table
Recasting
Writing isoformData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/isoform_exp.diff
Writing isoformExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading read group info in /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/isoforms.read_group_tracking
Writing isoformReplicateData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reshaping TSSData table
Recasting
Writing TSSData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/tss_group_exp.diff
Writing TSSExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/splicing.diff
Writing splicingDiffData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading read group info in /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/tss_groups.read_group_tracking
Writing TSSReplicateData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reshaping CDSData table
Recasting
Writing CDSData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/cds_exp.diff
Writing CDSExpDiffData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/cds.diff
Writing CDSDiffData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Reading read group info in /home/biocbuild/bbs-3.17-bioc/R/site-library/cummeRbund/extdata/cds.read_group_tracking
Writing CDSReplicateData table
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Indexing Tables...
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning in result_fetch(res@ptr, n = n) :
SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Scale for x is already present.
Adding another scale for x, which will replace the existing
scale.
Warning: call dbDisconnect() when finished working with a connection
Scale for x is already present.
Adding another scale for x, which will replace the existing
scale.
Warning: Removed 204 rows containing non-finite values
(`stat_density()`).
Warning: Removed 492 rows containing non-finite values
(`stat_density()`).
Warning: Removed 204 rows containing non-finite values
(`stat_density()`).
Warning: Removed 492 rows containing non-finite values
(`stat_density()`).
Warning: Removed 204 rows containing non-finite values
(`stat_density()`).
Warning: Removed 492 rows containing non-finite values
(`stat_density()`).
Warning: The dot-dot notation (`..scaled..`) was deprecated in ggplot2
3.4.0.
ℹ Please use `after_stat(scaled)` instead.
ℹ The deprecated feature was likely used in the cummeRbund
package.
Please report the issue to the authors.
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
`geom_smooth()` using formula = 'y ~ x'
Warning: Removed 54 rows containing missing values (`geom_point()`).
Warning: Removed 54 rows containing missing values (`geom_point()`).
Warning: Removed 54 rows containing missing values (`geom_point()`).
Warning: Removed 54 rows containing missing values (`geom_point()`).
Warning: Removed 54 rows containing missing values (`geom_point()`).
Warning: Removed 54 rows containing missing values (`geom_point()`).
Warning: Removed 40 rows containing missing values (`geom_point()`).
Warning: Removed 40 rows containing missing values (`geom_point()`).
Warning: Removed 40 rows containing missing values (`geom_point()`).
Getting gene information:
FPKM
Warning: Closing open result set, pending rows
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting isoforms information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting CDS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting TSS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting promoter information:
distData
Warning: Closing open result set, pending rows
Getting splicing information:
distData
Getting relCDS information:
distData
Getting gene information:
FPKM
Warning: Closing open result set, pending rows
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting isoforms information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting CDS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting TSS information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Counts
Getting promoter information:
distData
Warning: Closing open result set, pending rows
Getting splicing information:
distData
Getting relCDS information:
distData
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, rep_name as id variables
No id variables; using all as measure variables
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
Using tracking_id, rep_name as id variables
No id variables; using all as measure variables
Scale for colour is already present.
Adding another scale for colour, which will replace the existing
scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing
scale.
Killed
SUMMARY: processing the following file failed:
‘cummeRbund-manual.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/cummeRbund.Rcheck/00check.log’
for details.
cummeRbund.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cummeRbund ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)