Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:43 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 473/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cummeRbund 2.47.0 (landing page) Loyal A. Goff
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the cummeRbund package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cummeRbund.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: cummeRbund |
Version: 2.47.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cummeRbund.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cummeRbund_2.47.0.tar.gz |
StartedAt: 2024-08-26 19:53:31 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 20:00:31 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 420.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: cummeRbund.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cummeRbund.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cummeRbund_2.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cummeRbund.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cummeRbund/DESCRIPTION’ ... OK * this is package ‘cummeRbund’ version ‘2.47.0’ * 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 installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: R 1.3Mb extdata 5.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocGenerics’ ‘plyr’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: 'NMFN' 'cluster' 'rjson' 'stringr' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: 'S4Vectors' All declared Imports should be used. Packages in Depends field not imported from: 'Gviz' 'RSQLite' 'fastcluster' 'ggplot2' 'reshape2' 'rtracklayer' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .CVdensity: no visible global function definition for 'ggplot' .CVdensity: no visible global function definition for 'geom_density' .CVdensity: no visible global function definition for 'aes' .CVdensity: no visible binding for global variable 'CV' .CVdensity: no visible binding for global variable 'sample_name' .CVdensity: no visible global function definition for 'scale_x_log10' .MAplot: no visible global function definition for 'ggplot' .MAplot: no visible global function definition for 'geom_point' .MAplot: no visible global function definition for 'aes' .MAplot: no visible binding for global variable 'A' .MAplot: no visible binding for global variable 'M' .MAplot: no visible global function definition for 'stat_smooth' .MAplot: no visible global function definition for 'geom_hline' .MDSplot: no visible global function definition for 'cmdscale' .MDSplot: no visible global function definition for 'ggplot' .MDSplot: no visible global function definition for 'geom_point' .MDSplot: no visible global function definition for 'aes' .MDSplot: no visible binding for global variable 'M1' .MDSplot: no visible binding for global variable 'M2' .MDSplot: no visible global function definition for 'geom_text' .MDSplot: no visible global function definition for 'theme_bw' .PCAplot: no visible global function definition for 'prcomp' .PCAplot: no visible global function definition for 'ggplot' .PCAplot: no visible global function definition for 'aes_string' .PCAplot: no visible global function definition for 'geom_point' .PCAplot: no visible global function definition for 'aes' .PCAplot: no visible binding for global variable 'obsnames' .PCAplot: no visible global function definition for 'geom_hline' .PCAplot: no visible global function definition for 'geom_vline' .PCAplot: no visible global function definition for 'geom_text' .PCAplot: no visible binding for global variable 'v1' .PCAplot: no visible binding for global variable 'v2' .PCAplot: no visible binding for global variable 'varnames' .PCAplot: no visible global function definition for 'geom_segment' .PCAplot: no visible global function definition for 'arrow' .PCAplot: no visible global function definition for 'unit' .PCAplot: no visible global function definition for 'theme_bw' .QCTable: no visible global function definition for 'dbGetQuery' .addFeatures: no visible global function definition for 'make.db.names' .addFeatures: no visible global function definition for 'dbWriteTable' .addFeatures: no visible global function definition for 'dbGetQuery' .as.GRanges: no visible global function definition for 'GRanges' .as.GRanges: no visible global function definition for 'Rle' .as.GRanges: no visible global function definition for 'IRanges' .as.GRanges: no visible global function definition for 'elementMetadata' .as.GRanges: no visible global function definition for 'elementMetadata<-' .barplot: no visible global function definition for 'ggplot' .barplot: no visible global function definition for 'aes' .barplot: no visible binding for global variable 'sample_name' .barplot: no visible global function definition for 'geom_bar' .barplot: no visible global function definition for 'geom_point' .barplot: no visible global function definition for 'geom_errorbar' .barplot: no visible binding for global variable 'conf_lo' .barplot: no visible binding for global variable 'conf_hi' .barplot: no visible global function definition for 'scale_y_log10' .barplot: no visible global function definition for 'facet_wrap' .barplot: no visible global function definition for 'labs' .barplot: no visible global function definition for 'theme' .barplot: no visible global function definition for 'element_text' .barplot: no visible global function definition for 'ylab' .barplot: no visible global function definition for 'geom_text' .barplot: no visible binding for global variable 'quant_status' .barplot: no visible global function definition for 'scale_fill_hue' .barplot: no visible global function definition for 'scale_colour_manual' .boxplot: no visible global function definition for 'ggplot' .boxplot: no visible global function definition for 'geom_boxplot' .boxplot: no visible global function definition for 'aes' .boxplot: no visible binding for global variable 'condition' .boxplot: no visible global function definition for 'theme' .boxplot: no visible global function definition for 'element_text' .boxplot: no visible global function definition for 'scale_fill_hue' .checkReps: no visible global function definition for 'dbReadTable' .checkSamples: no visible global function definition for 'dbReadTable' .cluster: no visible global function definition for 'pam' .confidencePlot: no visible global function definition for 'ggplot' .confidencePlot: no visible global function definition for 'geom_point' .confidencePlot: no visible global function definition for 'aes' .confidencePlot: no visible binding for global variable 'CV' .confidencePlot: no visible global function definition for 'geom_smooth' .confidencePlot: no visible binding for global variable 'sample_name' .confidencePlot: no visible global function definition for 'geom_abline' .confidencePlot: no visible global function definition for 'scale_color_gradient' .confidencePlot: no visible global function definition for 'labs' .countMatrix: no visible global function definition for 'melt' .countMatrix: no visible global function definition for 'dcast' .cuff2db: no visible global function definition for 'import' .cuff2db: no visible global function definition for 'values' .cuff2db: no visible global function definition for 'seqnames' .cuff2db: no visible global function definition for 'start' .cuff2db: no visible global function definition for 'strand' .cuff2db: no visible global function definition for 'ranges' .cuff2db: no visible global function definition for 'end' .cuff2db: no visible global function definition for 'elementNROWS' .cuff2db: no visible global function definition for 'makeTxDb' .dendro: no visible global function definition for 'as.dendrogram' .dendro: no visible global function definition for 'hclust' .density: no visible global function definition for 'ggplot' .density: no visible global function definition for 'geom_density' .density: no visible global function definition for 'aes' .density: no visible binding for global variable 'condition' .density: no visible global function definition for 'scale_fill_hue' .density: no visible global function definition for 'scale_color_hue' .diffTable: no visible global function definition for 'melt' .diffTable: no visible global function definition for 'dcast' .dispersionPlot: no visible global function definition for 'ggplot' .dispersionPlot: no visible global function definition for 'geom_point' .dispersionPlot: no visible global function definition for 'aes' .dispersionPlot: no visible binding for global variable 'dispersion' .dispersionPlot: no visible binding for global variable 'sample_name' .dispersionPlot: no visible global function definition for 'facet_wrap' .dispersionPlot: no visible global function definition for 'scale_x_log10' .dispersionPlot: no visible global function definition for 'scale_y_log10' .distheat: no visible global function definition for 'hclust' .distheat: no visible global function definition for 'melt' .distheat: no visible global function definition for 'ggplot' .distheat: no visible global function definition for 'aes' .distheat: no visible binding for global variable 'X1' .distheat: no visible binding for global variable 'X2' .distheat: no visible binding for global variable 'value' .distheat: no visible global function definition for 'geom_tile' .distheat: no visible global function definition for 'scale_x_discrete' .distheat: no visible global function definition for 'scale_y_discrete' .distheat: no visible global function definition for 'theme' .distheat: no visible global function definition for 'element_text' .distheat: no visible global function definition for 'element_line' .distheat: no visible global function definition for 'element_rect' .distheat: no visible global function definition for 'scale_fill_gradient' .distheat: no visible global function definition for 'scale_fill_gradient2' .distheat: no visible global function definition for 'geom_text' .expressionPlot: no visible binding for global variable 'mean_cl_boot' .expressionPlot: no visible global function definition for 'ggplot' .expressionPlot: no visible global function definition for 'geom_line' .expressionPlot: no visible global function definition for 'aes' .expressionPlot: no visible binding for global variable 'sample_name' .expressionPlot: no visible binding for global variable 'tracking_id' .expressionPlot: no visible global function definition for 'geom_point' .expressionPlot: no visible global function definition for 'geom_errorbar' .expressionPlot: no visible binding for global variable 'conf_lo' .expressionPlot: no visible binding for global variable 'conf_hi' .expressionPlot: no visible global function definition for 'scale_y_log10' .expressionPlot: no visible binding for global variable 'quant_status' .expressionPlot: no visible global function definition for 'stat_summary' .expressionPlot: no visible global function definition for 'ylab' .expressionPlot: no visible global function definition for 'scale_fill_hue' .expressionPlot: no visible global function definition for 'scale_color_hue' .expressionPlot: no visible global function definition for 'labs' .expressionPlot: no visible global function definition for 'theme' .expressionPlot: no visible global function definition for 'element_text' .expressionPlot: no visible global function definition for 'facet_wrap' .fcheatmap: no visible binding for global variable 'dist' .fcheatmap: no visible global function definition for 'hclust' .fcheatmap: no visible global function definition for 'melt' .fcheatmap: no visible global function definition for 'ggplot' .fcheatmap: no visible global function definition for 'geom_rect' .fcheatmap: no visible global function definition for 'aes' .fcheatmap: no visible binding for global variable 'colInd' .fcheatmap: no visible binding for global variable 'rowInd' .fcheatmap: no visible binding for global variable 'value' .fcheatmap: no visible global function definition for 'scale_x_continuous' .fcheatmap: no visible global function definition for 'scale_y_continuous' .fcheatmap: no visible global function definition for 'theme' .fcheatmap: no visible global function definition for 'element_blank' .fcheatmap: no visible global function definition for 'element_line' .fcheatmap: no visible global function definition for 'element_rect' .fcheatmap: no visible global function definition for 'element_text' .fcheatmap: no visible global function definition for 'scale_fill_gradient' .fcheatmap: no visible global function definition for 'scale_fill_gradient2' .findGene: no visible global function definition for 'dbGetQuery' .findK: no visible global function definition for 'pam' .fpkmMatrix: no visible global function definition for 'melt' .fpkmMatrix: no visible global function definition for 'dcast' .fpkmSCVPlot : <anonymous>: no visible global function definition for 'sd' .fpkmSCVPlot: no visible global function definition for 'melt' .fpkmSCVPlot: no visible global function definition for 'ggplot' .fpkmSCVPlot: no visible global function definition for 'aes' .fpkmSCVPlot: no visible binding for global variable 'stdev' .fpkmSCVPlot: no visible global function definition for 'stat_smooth' .fpkmSCVPlot: no visible binding for global variable 'sample_name' .fpkmSCVPlot: no visible global function definition for 'scale_x_log10' .fpkmSCVPlot: no visible global function definition for 'scale_y_continuous' .fpkmSCVPlot: no visible global function definition for 'xlab' .fpkmSCVPlot: no visible global function definition for 'theme_bw' .fpkmSCVPlot: no visible global function definition for 'xlim' .fpkmSCVPlot: no visible global function definition for 'labs' .getCountMA: no visible global function definition for 'dbGetQuery' .getFeatures: no visible global function definition for 'dbSendQuery' .getFeatures: no visible global function definition for 'dbGetQuery' .getGene: no visible global function definition for 'dbSendQuery' .getGene: no visible global function definition for 'dbGetQuery' .getGeneId: no visible global function definition for 'dbGetQuery' .getGenes: no visible global function definition for 'dbSendQuery' .getGenes: no visible global function definition for 'dbGetQuery' .getGenome: no visible global function definition for 'dbGetQuery' .getLevels: no visible global function definition for 'dbGetQuery' .getMA: no visible global function definition for 'dbGetQuery' .getRepConditionLevels: no visible global function definition for 'dbGetQuery' .getRepLevels: no visible global function definition for 'dbGetQuery' .getSig: no visible global function definition for 'dbGetQuery' .getSig: no visible global function definition for 'p.adjust' .getSigTable: no visible global function definition for 'dbGetQuery' .getSigTable: no visible global function definition for 'p.adjust' .getSigTable: no visible global function definition for 'acast' .getSigTable: no visible global function definition for 'as.formula' .ggheat: no visible global function definition for 'hclust' .ggheat: no visible global function definition for 'melt' .ggheat: no visible global function definition for 'ggplot' .ggheat: no visible global function definition for 'geom_rect' .ggheat: no visible global function definition for 'aes' .ggheat: no visible binding for global variable 'colInd' .ggheat: no visible binding for global variable 'rowInd' .ggheat: no visible binding for global variable 'value' .ggheat: no visible global function definition for 'scale_x_continuous' .ggheat: no visible global function definition for 'scale_y_continuous' .ggheat: no visible global function definition for 'theme' .ggheat: no visible global function definition for 'element_blank' .ggheat: no visible global function definition for 'element_line' .ggheat: no visible global function definition for 'element_rect' .ggheat: no visible global function definition for 'element_text' .ggheat: no visible global function definition for 'scale_fill_gradient' .ggheat: no visible global function definition for 'scale_fill_gradient2' .hclustToJSON: no visible global function definition for 'toJSON' .heatmap: no visible global function definition for 'ggplot' .heatmap: no visible global function definition for 'geom_tile' .heatmap: no visible global function definition for 'aes' .heatmap: no visible binding for global variable 'tracking_id' .heatmap: no visible binding for global variable 'sample_name' .heatmap: no visible global function definition for 'scale_fill_gradient' .heatmap: no visible global function definition for 'theme' .heatmap: no visible global function definition for 'element_text' .ideogram: no visible global function definition for 'plotIdeogram' .loadGTF: no visible global function definition for 'import' .loadGTF: no visible global function definition for 'dbWriteTable' .makeGRanges: no visible global function definition for 'dbGetQuery' .makeGRanges: no visible global function definition for 'GRanges' .makeGRanges: no visible global function definition for 'IRanges' .makeGeneRegionTrack: no visible global function definition for 'GeneRegionTrack' .makeRnk: no visible global function definition for 'dbGetQuery' .makeRnk: no visible global function definition for 'write.table' .makeRnkTest: no visible global function definition for 'dbGetQuery' .makeRnkTest: no visible global function definition for 'write.table' .makeRnkTestStat: no visible global function definition for 'dbGetQuery' .makeRnkTestStat: no visible global function definition for 'write.table' .nmf: no visible global function definition for 'nnmf' .pie: no visible global function definition for 'ggplot' .pie: no visible global function definition for 'aes' .pie: no visible binding for global variable 'tracking_id' .pie: no visible global function definition for 'geom_bar' .pie: no visible global function definition for 'coord_polar' .pie: no visible global function definition for 'scale_fill_hue' .pie: no visible global function definition for 'scale_color_hue' .pie: no visible global function definition for 'theme_bw' .pie: no visible global function definition for 'facet_wrap' .pie: no visible global function definition for 'theme' .pie: no visible global function definition for 'element_blank' .plot: no visible global function definition for 'IdeogramTrack' .plot: no visible global function definition for 'GenomeAxisTrack' .plot: no visible global function definition for 'BiomartGeneRegionTrack' .plot: no visible global function definition for 'plotTracks' .plot2: no visible global function definition for 'theme_bw' .plot2: no visible global function definition for 'theme' .plot2: no visible global function definition for 'hasAxis<-' .plot2: no visible global function definition for 'ggplot' .plot2: no visible global function definition for 'tracks' .plotmatrix: no visible global function definition for 'aes' .plotmatrix: no visible binding for global variable 'x' .plotmatrix: no visible binding for global variable 'y' .plotmatrix: no visible global function definition for 'aes_string' .plotmatrix: no visible global function definition for 'ggplot' .plotmatrix: no visible global function definition for 'facet_grid' .plotmatrix: no visible global function definition for 'geom_hex' .plotmatrix: no visible global function definition for 'geom_point' .plotmatrix: no visible global function definition for 'stat_density' .plotmatrix: no visible binding for global variable '..scaled..' .ratioCluster: no visible global function definition for 'dist' .ratioCluster: no visible global function definition for 'pam' .recordGenome: no visible global function definition for 'dbSendQuery' .repCountMatrix: no visible global function definition for 'melt' .repCountMatrix: no visible global function definition for 'dcast' .repFpkmMatrix: no visible global function definition for 'melt' .repFpkmMatrix: no visible global function definition for 'dcast' .runInfo: no visible global function definition for 'dbGetQuery' .scatter: no visible global function definition for 'str_split_fixed' .scatter: no visible global function definition for 'ggplot' .scatter: no visible global function definition for 'aes_string' .scatter: no visible global function definition for 'geom_point' .scatter: no visible global function definition for 'geom_abline' .scatter: no visible global function definition for 'geom_rug' .scatter: no visible global function definition for 'stat_smooth' .scatter: no visible global function definition for 'geom_text' .scatter: no visible global function definition for 'scale_y_log10' .scatter: no visible global function definition for 'scale_x_log10' .scatter: no visible global function definition for 'ylab' .scatter: no visible global function definition for 'xlab' .scatter2: no visible global function definition for 'dbGetQuery' .scatter2: no visible global function definition for 'ggplot' .scatter2: no visible global function definition for 'theme_bw' .scatter2: no visible global function definition for 'aes_string' .scatter2: no visible global function definition for 'geom_point' .scatter2: no visible global function definition for 'aes' .scatter2: no visible binding for global variable 'significant' .scatter2: no visible global function definition for 'scale_color_manual' .scatter2: no visible global function definition for 'geom_abline' .scatter2: no visible global function definition for 'geom_rug' .scatter2: no visible global function definition for 'stat_smooth' .scatter2: no visible global function definition for 'geom_text' .scatter2: no visible global function definition for 'scale_y_log10' .scatter2: no visible global function definition for 'scale_x_log10' .scatter2: no visible global function definition for 'labs' .scatterMat: no visible global function definition for 'geom_abline' .scatterMat: no visible global function definition for 'theme_bw' .scatterMat: no visible global function definition for 'ylab' .scatterMat: no visible global function definition for 'xlab' .sigMatrix: no visible global function definition for 'dbGetQuery' .sigMatrix: no visible global function definition for 'p.adjust' .sigMatrix: no visible global function definition for 'order.dendrogram' .sigMatrix: no visible global function definition for 'as.dendrogram' .sigMatrix: no visible global function definition for 'hclust' .sigMatrix: no visible global function definition for 'ggplot' .sigMatrix: no visible global function definition for 'aes' .sigMatrix: no visible binding for global variable 'sample_1' .sigMatrix: no visible binding for global variable 'sample_2' .sigMatrix: no visible global function definition for 'stat_sum' .sigMatrix: no visible binding for global variable '..n..' .sigMatrix: no visible global function definition for 'scale_fill_continuous' .sigMatrix: no visible global function definition for 'expand_limits' .sigMatrix: no visible global function definition for 'theme_bw' .sigMatrix: no visible global function definition for 'labs' .sigMatrix: no visible global function definition for 'theme' .sigMatrix: no visible global function definition for 'element_text' .sigMatrix: no visible global function definition for 'coord_equal' .statsMatrix: no visible global function definition for 'dbGetQuery' .values: no visible global function definition for 'dbGetQuery' .varModel: no visible global function definition for 'dbGetQuery' .volcano: no visible global function definition for 'ggplot' .volcano: no visible global function definition for 'geom_point' .volcano: no visible global function definition for 'aes' .volcano: no visible binding for global variable 'log2_fold_change' .volcano: no visible binding for global variable 'p_value' .volcano: no visible binding for global variable 'significant' .volcano: no visible global function definition for 'labs' .volcano: no visible global function definition for 'scale_x_continuous' .volcano: no visible global function definition for 'scale_colour_manual' .volcanoMatrix: no visible global function definition for 'aes' .volcanoMatrix: no visible global function definition for 'aes_string' .volcanoMatrix: no visible global function definition for 'ggplot' .volcanoMatrix: no visible global function definition for 'geom_point' .volcanoMatrix: no visible global function definition for 'scale_colour_manual' .volcanoMatrix: no visible global function definition for 'facet_grid' .volcanoMatrix: no visible global function definition for 'geom_vline' .volcanoMatrix: no visible global function definition for 'theme_bw' .volcanoMatrix: no visible global function definition for 'xlab' .volcanoMatrix: no visible global function definition for 'ylab' JSdist: no visible global function definition for 'as.dist' bulk_insert: no visible global function definition for 'dbBegin' bulk_insert: no visible global function definition for 'dbGetPreparedQuery' bulk_insert: no visible global function definition for 'dbCommit' createDB_noIndex: no visible global function definition for 'dbDriver' createDB_noIndex: no visible global function definition for 'dbConnect' createDB_noIndex : <anonymous>: no visible global function definition for 'dbGetQuery' createIndices: no visible global function definition for 'dbDriver' createIndices: no visible global function definition for 'dbConnect' createIndices : <anonymous>: no visible global function definition for 'dbGetQuery' csClusterPlot: no visible binding for global variable 'mean_cl_boot' csClusterPlot: no visible global function definition for 'melt' csClusterPlot: no visible global function definition for 'ggplot' csClusterPlot: no visible global function definition for 'geom_line' csClusterPlot: no visible global function definition for 'aes' csClusterPlot: no visible binding for global variable 'variable' csClusterPlot: no visible binding for global variable 'value' csClusterPlot: no visible binding for global variable 'cluster' csClusterPlot: no visible binding for global variable 'ids' csClusterPlot: no visible global function definition for 'theme_bw' csClusterPlot: no visible global function definition for 'facet_wrap' csClusterPlot: no visible global function definition for 'stat_summary' csClusterPlot: no visible global function definition for 'scale_y_log10' csClusterPlot: no visible global function definition for 'scale_color_hue' csClusterPlot: no visible global function definition for 'theme' csClusterPlot: no visible global function definition for 'element_text' expressionPlot: no visible binding for global variable 'mean_cl_boot' loadCDS: no visible binding for global variable 'read.table' loadCDS: no visible global function definition for 'make.db.names' loadCDS: no visible global function definition for 'dbReadTable' loadCDS: no visible global function definition for 'melt' loadCDS: no visible global function definition for 'dcast' loadGenes: no visible binding for global variable 'read.table' loadGenes: no visible global function definition for 'make.db.names' loadGenes: no visible global function definition for 'dbReadTable' loadGenes: no visible global function definition for 'melt' loadGenes: no visible global function definition for 'dcast' loadIsoforms: no visible binding for global variable 'read.table' loadIsoforms: no visible global function definition for 'make.db.names' loadIsoforms: no visible global function definition for 'dbReadTable' loadIsoforms: no visible global function definition for 'melt' loadIsoforms: no visible global function definition for 'dcast' loadRepTable: no visible global function definition for 'read.delim' loadRepTable: no visible global function definition for 'make.db.names' loadRunInfo: no visible binding for global variable 'read.table' loadTSS: no visible binding for global variable 'read.table' loadTSS: no visible global function definition for 'make.db.names' loadTSS: no visible global function definition for 'dbReadTable' loadTSS: no visible global function definition for 'melt' loadTSS: no visible global function definition for 'dcast' loadVarModelTable: no visible global function definition for 'read.delim' loadVarModelTable: no visible global function definition for 'make.db.names' populateSampleTable: no visible global function definition for 'make.db.names' populateSampleTable: no visible global function definition for 'dbWriteTable' readCufflinks: no visible global function definition for 'dbConnect' readCufflinks: no visible global function definition for 'dbDriver' MAplot,CuffData: no visible global function definition for 'ggplot' MAplot,CuffData: no visible global function definition for 'geom_point' MAplot,CuffData: no visible global function definition for 'aes' MAplot,CuffData: no visible binding for global variable 'A' MAplot,CuffData: no visible binding for global variable 'M' MAplot,CuffData: no visible global function definition for 'stat_smooth' MAplot,CuffData: no visible global function definition for 'geom_hline' MDSplot,CuffData: no visible global function definition for 'cmdscale' MDSplot,CuffData: no visible global function definition for 'ggplot' MDSplot,CuffData: no visible global function definition for 'geom_point' MDSplot,CuffData: no visible global function definition for 'aes' MDSplot,CuffData: no visible binding for global variable 'M1' MDSplot,CuffData: no visible binding for global variable 'M2' MDSplot,CuffData: no visible global function definition for 'geom_text' MDSplot,CuffData: no visible global function definition for 'theme_bw' MDSplot,CuffFeatureSet: no visible global function definition for 'cmdscale' MDSplot,CuffFeatureSet: no visible global function definition for 'ggplot' MDSplot,CuffFeatureSet: no visible global function definition for 'geom_point' MDSplot,CuffFeatureSet: no visible global function definition for 'aes' MDSplot,CuffFeatureSet: no visible binding for global variable 'M1' MDSplot,CuffFeatureSet: no visible binding for global variable 'M2' MDSplot,CuffFeatureSet: no visible global function definition for 'geom_text' MDSplot,CuffFeatureSet: no visible global function definition for 'theme_bw' PCAplot,CuffData: no visible global function definition for 'prcomp' PCAplot,CuffData: no visible global function definition for 'ggplot' PCAplot,CuffData: no visible global function definition for 'aes_string' PCAplot,CuffData: no visible global function definition for 'geom_point' PCAplot,CuffData: no visible global function definition for 'aes' PCAplot,CuffData: no visible binding for global variable 'obsnames' PCAplot,CuffData: no visible global function definition for 'geom_hline' PCAplot,CuffData: no visible global function definition for 'geom_vline' PCAplot,CuffData: no visible global function definition for 'geom_text' PCAplot,CuffData: no visible binding for global variable 'v1' PCAplot,CuffData: no visible binding for global variable 'v2' PCAplot,CuffData: no visible binding for global variable 'varnames' PCAplot,CuffData: no visible global function definition for 'geom_segment' PCAplot,CuffData: no visible global function definition for 'arrow' PCAplot,CuffData: no visible global function definition for 'unit' PCAplot,CuffData: no visible global function definition for 'theme_bw' PCAplot,CuffFeatureSet: no visible global function definition for 'prcomp' PCAplot,CuffFeatureSet: no visible global function definition for 'ggplot' PCAplot,CuffFeatureSet: no visible global function definition for 'aes_string' PCAplot,CuffFeatureSet: no visible global function definition for 'geom_point' PCAplot,CuffFeatureSet: no visible global function definition for 'aes' PCAplot,CuffFeatureSet: no visible binding for global variable 'obsnames' PCAplot,CuffFeatureSet: no visible global function definition for 'geom_hline' PCAplot,CuffFeatureSet: no visible global function definition for 'geom_vline' PCAplot,CuffFeatureSet: no visible global function definition for 'geom_text' PCAplot,CuffFeatureSet: no visible binding for global variable 'v1' PCAplot,CuffFeatureSet: no visible binding for global variable 'v2' PCAplot,CuffFeatureSet: no visible binding for global variable 'varnames' PCAplot,CuffFeatureSet: no visible global function definition for 'geom_segment' PCAplot,CuffFeatureSet: no visible global function definition for 'arrow' PCAplot,CuffFeatureSet: no visible global function definition for 'unit' PCAplot,CuffFeatureSet: no visible global function definition for 'theme_bw' addFeatures,CuffData: no visible global function definition for 'make.db.names' addFeatures,CuffData: no visible global function definition for 'dbWriteTable' addFeatures,CuffData: no visible global function definition for 'dbGetQuery' addFeatures,CuffSet: no visible global function definition for 'make.db.names' addFeatures,CuffSet: no visible global function definition for 'dbWriteTable' addFeatures,CuffSet: no visible global function definition for 'dbGetQuery' annotation,CuffData: no visible global function definition for 'dbGetQuery' coerce,CuffGene-GRanges: no visible global function definition for 'GRanges' coerce,CuffGene-GRanges: no visible global function definition for 'Rle' coerce,CuffGene-GRanges: no visible global function definition for 'IRanges' coerce,CuffGene-GRanges: no visible global function definition for 'elementMetadata' coerce,CuffGene-GRanges: no visible global function definition for 'elementMetadata<-' count,CuffData: no visible global function definition for 'dbGetQuery' countMatrix,CuffData: no visible global function definition for 'dbGetQuery' countMatrix,CuffFeatureSet: no visible global function definition for 'melt' countMatrix,CuffFeatureSet: no visible global function definition for 'dcast' csBoxplot,CuffData: no visible global function definition for 'ggplot' csBoxplot,CuffData: no visible global function definition for 'geom_boxplot' csBoxplot,CuffData: no visible global function definition for 'aes' csBoxplot,CuffData: no visible binding for global variable 'condition' csBoxplot,CuffData: no visible global function definition for 'theme' csBoxplot,CuffData: no visible global function definition for 'element_text' csBoxplot,CuffData: no visible global function definition for 'scale_fill_hue' csCluster,CuffFeatureSet: no visible global function definition for 'pam' csDendro,CuffData: no visible global function definition for 'as.dendrogram' csDendro,CuffData: no visible global function definition for 'hclust' csDendro,CuffFeatureSet: no visible global function definition for 'as.dendrogram' csDendro,CuffFeatureSet: no visible global function definition for 'hclust' csDensity,CuffData: no visible global function definition for 'ggplot' csDensity,CuffData: no visible global function definition for 'geom_density' csDensity,CuffData: no visible global function definition for 'aes' csDensity,CuffData: no visible binding for global variable 'condition' csDensity,CuffData: no visible global function definition for 'labs' csDensity,CuffData: no visible global function definition for 'scale_fill_hue' csDensity,CuffData: no visible global function definition for 'scale_color_hue' csDensity,CuffFeatureSet: no visible global function definition for 'ggplot' csDensity,CuffFeatureSet: no visible global function definition for 'geom_density' csDensity,CuffFeatureSet: no visible global function definition for 'aes' csDensity,CuffFeatureSet: no visible binding for global variable 'condition' csDensity,CuffFeatureSet: no visible global function definition for 'scale_fill_hue' csDensity,CuffFeatureSet: no visible global function definition for 'scale_color_hue' csDistHeat,CuffData: no visible global function definition for 'hclust' csDistHeat,CuffData: no visible global function definition for 'melt' csDistHeat,CuffData: no visible global function definition for 'ggplot' csDistHeat,CuffData: no visible global function definition for 'aes' csDistHeat,CuffData: no visible binding for global variable 'X1' csDistHeat,CuffData: no visible binding for global variable 'X2' csDistHeat,CuffData: no visible binding for global variable 'value' csDistHeat,CuffData: no visible global function definition for 'geom_tile' csDistHeat,CuffData: no visible global function definition for 'scale_x_discrete' csDistHeat,CuffData: no visible global function definition for 'scale_y_discrete' csDistHeat,CuffData: no visible global function definition for 'theme' csDistHeat,CuffData: no visible global function definition for 'element_text' csDistHeat,CuffData: no visible global function definition for 'element_line' csDistHeat,CuffData: no visible global function definition for 'element_rect' csDistHeat,CuffData: no visible global function definition for 'scale_fill_gradient' csDistHeat,CuffData: no visible global function definition for 'scale_fill_gradient2' csDistHeat,CuffData: no visible global function definition for 'geom_text' csDistHeat,CuffFeatureSet: no visible global function definition for 'hclust' csDistHeat,CuffFeatureSet: no visible global function definition for 'melt' csDistHeat,CuffFeatureSet: no visible global function definition for 'ggplot' csDistHeat,CuffFeatureSet: no visible global function definition for 'aes' csDistHeat,CuffFeatureSet: no visible binding for global variable 'X1' csDistHeat,CuffFeatureSet: no visible binding for global variable 'X2' csDistHeat,CuffFeatureSet: no visible binding for global variable 'value' csDistHeat,CuffFeatureSet: no visible global function definition for 'geom_tile' csDistHeat,CuffFeatureSet: no visible global function definition for 'scale_x_discrete' csDistHeat,CuffFeatureSet: no visible global function definition for 'scale_y_discrete' csDistHeat,CuffFeatureSet: no visible global function definition for 'theme' csDistHeat,CuffFeatureSet: no visible global function definition for 'element_text' csDistHeat,CuffFeatureSet: no visible global function definition for 'element_line' csDistHeat,CuffFeatureSet: no visible global function definition for 'element_rect' csDistHeat,CuffFeatureSet: no visible global function definition for 'scale_fill_gradient' csDistHeat,CuffFeatureSet: no visible global function definition for 'scale_fill_gradient2' csDistHeat,CuffFeatureSet: no visible global function definition for 'geom_text' csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global variable 'dist' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'hclust' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'melt' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'ggplot' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'geom_rect' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'aes' csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global variable 'colInd' csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global variable 'rowInd' csFoldChangeHeatmap,CuffFeatureSet: no visible binding for global variable 'value' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'scale_x_continuous' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'scale_y_continuous' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'theme' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'element_blank' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'element_line' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'element_rect' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'element_text' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'scale_fill_gradient' csFoldChangeHeatmap,CuffFeatureSet: no visible global function definition for 'scale_fill_gradient2' csHeatmap,CuffFeatureSet: no visible global function definition for 'hclust' csHeatmap,CuffFeatureSet: no visible global function definition for 'melt' csHeatmap,CuffFeatureSet: no visible global function definition for 'ggplot' csHeatmap,CuffFeatureSet: no visible global function definition for 'geom_rect' csHeatmap,CuffFeatureSet: no visible global function definition for 'aes' csHeatmap,CuffFeatureSet: no visible binding for global variable 'colInd' csHeatmap,CuffFeatureSet: no visible binding for global variable 'rowInd' csHeatmap,CuffFeatureSet: no visible binding for global variable 'value' csHeatmap,CuffFeatureSet: no visible global function definition for 'scale_x_continuous' csHeatmap,CuffFeatureSet: no visible global function definition for 'scale_y_continuous' csHeatmap,CuffFeatureSet: no visible global function definition for 'theme' csHeatmap,CuffFeatureSet: no visible global function definition for 'element_blank' csHeatmap,CuffFeatureSet: no visible global function definition for 'element_line' csHeatmap,CuffFeatureSet: no visible global function definition for 'element_rect' csHeatmap,CuffFeatureSet: no visible global function definition for 'element_text' csHeatmap,CuffFeatureSet: no visible global function definition for 'scale_fill_gradient' csHeatmap,CuffFeatureSet: no visible global function definition for 'scale_fill_gradient2' csNMF,CuffData: no visible global function definition for 'nnmf' csNMF,CuffFeatureSet: no visible global function definition for 'nnmf' csPie,CuffGene: no visible global function definition for 'ggplot' csPie,CuffGene: no visible global function definition for 'aes' csPie,CuffGene: no visible binding for global variable 'tracking_id' csPie,CuffGene: no visible global function definition for 'geom_bar' csPie,CuffGene: no visible global function definition for 'coord_polar' csPie,CuffGene: no visible global function definition for 'scale_fill_hue' csPie,CuffGene: no visible global function definition for 'scale_color_hue' csPie,CuffGene: no visible global function definition for 'theme_bw' csPie,CuffGene: no visible global function definition for 'facet_wrap' csPie,CuffGene: no visible global function definition for 'theme' csPie,CuffGene: no visible global function definition for 'element_blank' csScatter,CuffData: no visible global function definition for 'str_split_fixed' csScatter,CuffData: no visible global function definition for 'ggplot' csScatter,CuffData: no visible global function definition for 'aes_string' csScatter,CuffData: no visible global function definition for 'geom_point' csScatter,CuffData: no visible global function definition for 'geom_abline' csScatter,CuffData: no visible global function definition for 'geom_rug' csScatter,CuffData: no visible global function definition for 'stat_smooth' csScatter,CuffData: no visible global function definition for 'geom_text' csScatter,CuffData: no visible global function definition for 'scale_y_log10' csScatter,CuffData: no visible global function definition for 'scale_x_log10' csScatter,CuffData: no visible global function definition for 'labs' csScatter,CuffFeatureSet: no visible global function definition for 'str_split_fixed' csScatter,CuffFeatureSet: no visible global function definition for 'ggplot' csScatter,CuffFeatureSet: no visible global function definition for 'aes_string' csScatter,CuffFeatureSet: no visible global function definition for 'geom_point' csScatter,CuffFeatureSet: no visible global function definition for 'geom_abline' csScatter,CuffFeatureSet: no visible global function definition for 'geom_rug' csScatter,CuffFeatureSet: no visible global function definition for 'stat_smooth' csScatter,CuffFeatureSet: no visible global function definition for 'geom_text' csScatter,CuffFeatureSet: no visible global function definition for 'scale_y_log10' csScatter,CuffFeatureSet: no visible global function definition for 'scale_x_log10' csScatter,CuffFeatureSet: no visible global function definition for 'ylab' csScatter,CuffFeatureSet: no visible global function definition for 'xlab' csScatterMatrix,CuffData: no visible global function definition for 'geom_abline' csScatterMatrix,CuffData: no visible global function definition for 'theme_bw' csScatterMatrix,CuffData: no visible global function definition for 'ylab' csScatterMatrix,CuffData: no visible global function definition for 'xlab' csVolcano,CuffData: no visible global function definition for 'ggplot' csVolcano,CuffData: no visible global function definition for 'geom_point' csVolcano,CuffData: no visible global function definition for 'aes' csVolcano,CuffData: no visible binding for global variable 'log2_fold_change' csVolcano,CuffData: no visible binding for global variable 'p_value' csVolcano,CuffData: no visible binding for global variable 'significant' csVolcano,CuffData: no visible global function definition for 'theme_bw' csVolcano,CuffData: no visible global function definition for 'labs' csVolcano,CuffData: no visible global function definition for 'scale_colour_manual' csVolcano,CuffData: no visible global function definition for 'scale_x_continuous' csVolcano,CuffData: no visible global function definition for 'xlab' csVolcano,CuffData: no visible global function definition for 'ylab' csVolcano,CuffFeatureSet: no visible global function definition for 'ggplot' csVolcano,CuffFeatureSet: no visible global function definition for 'geom_point' csVolcano,CuffFeatureSet: no visible global function definition for 'aes' csVolcano,CuffFeatureSet: no visible binding for global variable 'log2_fold_change' csVolcano,CuffFeatureSet: no visible binding for global variable 'p_value' csVolcano,CuffFeatureSet: no visible binding for global variable 'significant' csVolcano,CuffFeatureSet: no visible global function definition for 'labs' csVolcano,CuffFeatureSet: no visible global function definition for 'scale_x_continuous' csVolcano,CuffFeatureSet: no visible global function definition for 'scale_colour_manual' csVolcanoMatrix,CuffData: no visible global function definition for 'aes' csVolcanoMatrix,CuffData: no visible global function definition for 'aes_string' csVolcanoMatrix,CuffData: no visible global function definition for 'ggplot' csVolcanoMatrix,CuffData: no visible global function definition for 'geom_point' csVolcanoMatrix,CuffData: no visible global function definition for 'scale_colour_manual' csVolcanoMatrix,CuffData: no visible global function definition for 'facet_grid' csVolcanoMatrix,CuffData: no visible global function definition for 'geom_vline' csVolcanoMatrix,CuffData: no visible global function definition for 'theme_bw' csVolcanoMatrix,CuffData: no visible global function definition for 'xlab' csVolcanoMatrix,CuffData: no visible global function definition for 'ylab' diffData,CuffData: no visible global function definition for 'dbGetQuery' diffTable,CuffData: no visible global function definition for 'melt' diffTable,CuffData: no visible global function definition for 'dcast' diffTable,CuffFeatureSet: no visible global function definition for 'melt' diffTable,CuffFeatureSet: no visible global function definition for 'dcast' dim,CuffData: no visible global function definition for 'dbGetQuery' dim,CuffDist: no visible global function definition for 'dbGetQuery' dispersionPlot,CuffData: no visible global function definition for 'ggplot' dispersionPlot,CuffData: no visible global function definition for 'geom_point' dispersionPlot,CuffData: no visible global function definition for 'aes' dispersionPlot,CuffData: no visible binding for global variable 'dispersion' dispersionPlot,CuffData: no visible binding for global variable 'sample_name' dispersionPlot,CuffData: no visible global function definition for 'facet_wrap' dispersionPlot,CuffData: no visible global function definition for 'scale_x_log10' dispersionPlot,CuffData: no visible global function definition for 'scale_y_log10' dispersionPlot,CuffSet: no visible global function definition for 'ggplot' dispersionPlot,CuffSet: no visible global function definition for 'geom_point' dispersionPlot,CuffSet: no visible global function definition for 'aes' dispersionPlot,CuffSet: no visible binding for global variable 'compatible_count_mean' dispersionPlot,CuffSet: no visible binding for global variable 'compatible_count_var' dispersionPlot,CuffSet: no visible binding for global variable 'condition' dispersionPlot,CuffSet: no visible global function definition for 'geom_line' dispersionPlot,CuffSet: no visible binding for global variable 'fitted_var' dispersionPlot,CuffSet: no visible global function definition for 'facet_wrap' dispersionPlot,CuffSet: no visible global function definition for 'scale_y_log10' dispersionPlot,CuffSet: no visible global function definition for 'scale_x_log10' dispersionPlot,CuffSet: no visible global function definition for 'theme_bw' dispersionPlot,CuffSet: no visible global function definition for 'guides' distValues,CuffDist: no visible global function definition for 'dbGetQuery' expressionBarplot,CuffFeature: no visible global function definition for 'ggplot' expressionBarplot,CuffFeature: no visible global function definition for 'aes' expressionBarplot,CuffFeature: no visible binding for global variable 'sample_name' expressionBarplot,CuffFeature: no visible global function definition for 'geom_bar' expressionBarplot,CuffFeature: no visible global function definition for 'geom_point' expressionBarplot,CuffFeature: no visible global function definition for 'geom_errorbar' expressionBarplot,CuffFeature: no visible binding for global variable 'conf_lo' expressionBarplot,CuffFeature: no visible binding for global variable 'conf_hi' expressionBarplot,CuffFeature: no visible global function definition for 'scale_y_log10' expressionBarplot,CuffFeature: no visible global function definition for 'facet_wrap' expressionBarplot,CuffFeature: no visible global function definition for 'labs' expressionBarplot,CuffFeature: no visible global function definition for 'theme' expressionBarplot,CuffFeature: no visible global function definition for 'element_text' expressionBarplot,CuffFeature: no visible global function definition for 'ylab' expressionBarplot,CuffFeature: no visible global function definition for 'geom_text' expressionBarplot,CuffFeature: no visible binding for global variable 'quant_status' expressionBarplot,CuffFeature: no visible global function definition for 'scale_fill_hue' expressionBarplot,CuffFeature: no visible global function definition for 'scale_colour_manual' expressionBarplot,CuffFeatureSet: no visible global function definition for 'position_dodge' expressionBarplot,CuffFeatureSet: no visible global function definition for 'ggplot' expressionBarplot,CuffFeatureSet: no visible global function definition for 'aes' expressionBarplot,CuffFeatureSet: no visible binding for global variable 'tracking_id' expressionBarplot,CuffFeatureSet: no visible binding for global variable 'sample_name' expressionBarplot,CuffFeatureSet: no visible global function definition for 'geom_bar' expressionBarplot,CuffFeatureSet: no visible global function definition for 'geom_errorbar' expressionBarplot,CuffFeatureSet: no visible binding for global variable 'conf_lo' expressionBarplot,CuffFeatureSet: no visible binding for global variable 'conf_hi' expressionBarplot,CuffFeatureSet: no visible global function definition for 'scale_y_log10' expressionBarplot,CuffFeatureSet: no visible global function definition for 'geom_text' expressionBarplot,CuffFeatureSet: no visible global function definition for 'scale_x_discrete' expressionBarplot,CuffFeatureSet: no visible global function definition for 'theme' expressionBarplot,CuffFeatureSet: no visible global function definition for 'element_text' expressionBarplot,CuffFeatureSet: no visible global function definition for 'ylab' expressionBarplot,CuffFeatureSet: no visible global function definition for 'scale_fill_hue' expressionBarplot,CuffFeatureSet: no visible global function definition for 'scale_color_hue' expressionBarplot,CuffFeatureSet: no visible global function definition for 'scale_colour_manual' expressionPlot,CuffFeature: no visible binding for global variable 'mean_cl_boot' expressionPlot,CuffFeature: no visible global function definition for 'ggplot' expressionPlot,CuffFeature: no visible global function definition for 'geom_line' expressionPlot,CuffFeature: no visible global function definition for 'aes' expressionPlot,CuffFeature: no visible binding for global variable 'sample_name' expressionPlot,CuffFeature: no visible binding for global variable 'tracking_id' expressionPlot,CuffFeature: no visible global function definition for 'geom_point' expressionPlot,CuffFeature: no visible global function definition for 'geom_errorbar' expressionPlot,CuffFeature: no visible binding for global variable 'conf_lo' expressionPlot,CuffFeature: no visible binding for global variable 'conf_hi' expressionPlot,CuffFeature: no visible global function definition for 'scale_y_log10' expressionPlot,CuffFeature: no visible binding for global variable 'quant_status' expressionPlot,CuffFeature: no visible global function definition for 'stat_summary' expressionPlot,CuffFeature: no visible global function definition for 'ylab' expressionPlot,CuffFeature: no visible global function definition for 'scale_fill_hue' expressionPlot,CuffFeature: no visible global function definition for 'scale_color_hue' expressionPlot,CuffFeature: no visible global function definition for 'labs' expressionPlot,CuffFeature: no visible global function definition for 'theme' expressionPlot,CuffFeature: no visible global function definition for 'element_text' expressionPlot,CuffFeature: no visible global function definition for 'facet_wrap' expressionPlot,CuffFeatureSet: no visible binding for global variable 'mean_cl_boot' expressionPlot,CuffFeatureSet: no visible global function definition for 'ggplot' expressionPlot,CuffFeatureSet: no visible global function definition for 'geom_line' expressionPlot,CuffFeatureSet: no visible global function definition for 'aes' expressionPlot,CuffFeatureSet: no visible binding for global variable 'sample_name' expressionPlot,CuffFeatureSet: no visible binding for global variable 'tracking_id' expressionPlot,CuffFeatureSet: no visible global function definition for 'geom_point' expressionPlot,CuffFeatureSet: no visible global function definition for 'geom_errorbar' expressionPlot,CuffFeatureSet: no visible binding for global variable 'conf_lo' expressionPlot,CuffFeatureSet: no visible binding for global variable 'conf_hi' expressionPlot,CuffFeatureSet: no visible binding for global variable 'quant_status' expressionPlot,CuffFeatureSet: no visible global function definition for 'scale_y_log10' expressionPlot,CuffFeatureSet: no visible global function definition for 'stat_summary' expressionPlot,CuffFeatureSet: no visible global function definition for 'ylab' featureNames,CuffData: no visible global function definition for 'dbGetQuery' findGene,CuffSet: no visible global function definition for 'dbGetQuery' fpkm,CuffData: no visible global function definition for 'dbGetQuery' fpkmMatrix,CuffData: no visible global function definition for 'dbGetQuery' fpkmMatrix,CuffFeature: no visible global function definition for 'melt' fpkmMatrix,CuffFeature: no visible global function definition for 'dcast' fpkmMatrix,CuffFeatureSet: no visible global function definition for 'melt' fpkmMatrix,CuffFeatureSet: no visible global function definition for 'dcast' fpkmSCVPlot,CuffData : <anonymous>: no visible global function definition for 'sd' fpkmSCVPlot,CuffData: no visible global function definition for 'melt' fpkmSCVPlot,CuffData: no visible global function definition for 'ggplot' fpkmSCVPlot,CuffData: no visible global function definition for 'aes' fpkmSCVPlot,CuffData: no visible binding for global variable 'stdev' fpkmSCVPlot,CuffData: no visible global function definition for 'stat_smooth' fpkmSCVPlot,CuffData: no visible binding for global variable 'sample_name' fpkmSCVPlot,CuffData: no visible global function definition for 'scale_x_log10' fpkmSCVPlot,CuffData: no visible global function definition for 'scale_y_continuous' fpkmSCVPlot,CuffData: no visible global function definition for 'xlab' fpkmSCVPlot,CuffData: no visible global function definition for 'theme_bw' fpkmSCVPlot,CuffData: no visible global function definition for 'xlim' fpkmSCVPlot,CuffData: no visible global function definition for 'labs' genePlot,CuffGene: no visible global function definition for 'IdeogramTrack' genePlot,CuffGene: no visible global function definition for 'GenomeAxisTrack' genePlot,CuffGene: no visible global function definition for 'BiomartGeneRegionTrack' genePlot,CuffGene: no visible global function definition for 'plotTracks' getFeatures,CuffSet: no visible global function definition for 'dbSendQuery' getFeatures,CuffSet: no visible global function definition for 'dbGetQuery' getGene,CuffSet: no visible global function definition for 'dbSendQuery' getGene,CuffSet: no visible global function definition for 'dbGetQuery' getGeneId,CuffSet: no visible global function definition for 'dbGetQuery' getGenes,CuffSet: no visible global function definition for 'dbSendQuery' getGenes,CuffSet: no visible global function definition for 'dbGetQuery' getLevels,CuffData: no visible global function definition for 'dbGetQuery' getLevels,CuffSet: no visible global function definition for 'dbGetQuery' getRepLevels,CuffData: no visible global function definition for 'dbGetQuery' getRepLevels,CuffSet: no visible global function definition for 'dbGetQuery' getSig,CuffSet: no visible global function definition for 'dbGetQuery' getSig,CuffSet: no visible global function definition for 'p.adjust' getSigTable,CuffSet: no visible global function definition for 'dbGetQuery' getSigTable,CuffSet: no visible global function definition for 'p.adjust' getSigTable,CuffSet: no visible global function definition for 'acast' getSigTable,CuffSet: no visible global function definition for 'as.formula' makeGRanges,CuffSet: no visible global function definition for 'dbGetQuery' makeGRanges,CuffSet: no visible global function definition for 'GRanges' makeGRanges,CuffSet: no visible global function definition for 'IRanges' makeGeneRegionTrack,CuffGene: no visible global function definition for 'GeneRegionTrack' makeRnk,CuffData: no visible global function definition for 'dbGetQuery' makeRnk,CuffData: no visible global function definition for 'write.table' repCountMatrix,CuffData: no visible global function definition for 'dbGetQuery' repCountMatrix,CuffFeatureSet: no visible global function definition for 'melt' repCountMatrix,CuffFeatureSet: no visible global function definition for 'dcast' repFpkm,CuffData: no visible global function definition for 'dbGetQuery' repFpkmMatrix,CuffData: no visible global function definition for 'dbGetQuery' repFpkmMatrix,CuffFeature: no visible global function definition for 'melt' repFpkmMatrix,CuffFeature: no visible global function definition for 'dcast' repFpkmMatrix,CuffFeatureSet: no visible global function definition for 'melt' repFpkmMatrix,CuffFeatureSet: no visible global function definition for 'dcast' replicates,CuffData: no visible global function definition for 'dbReadTable' replicates,CuffSet: no visible global function definition for 'dbGetQuery' runInfo,CuffSet: no visible global function definition for 'dbGetQuery' samples,CuffData: no visible global function definition for 'dbReadTable' samples,CuffDist: no visible global function definition for 'dbReadTable' samples,CuffSet: no visible global function definition for 'dbGetQuery' sigMatrix,CuffSet: no visible global function definition for 'dbGetQuery' sigMatrix,CuffSet: no visible global function definition for 'p.adjust' sigMatrix,CuffSet: no visible global function definition for 'order.dendrogram' sigMatrix,CuffSet: no visible global function definition for 'as.dendrogram' sigMatrix,CuffSet: no visible global function definition for 'hclust' sigMatrix,CuffSet: no visible global function definition for 'ggplot' sigMatrix,CuffSet: no visible global function definition for 'aes' sigMatrix,CuffSet: no visible binding for global variable 'sample_1' sigMatrix,CuffSet: no visible binding for global variable 'sample_2' sigMatrix,CuffSet: no visible global function definition for 'stat_sum' sigMatrix,CuffSet: no visible binding for global variable '..n..' sigMatrix,CuffSet: no visible global function definition for 'scale_fill_continuous' sigMatrix,CuffSet: no visible global function definition for 'expand_limits' sigMatrix,CuffSet: no visible global function definition for 'theme_bw' sigMatrix,CuffSet: no visible global function definition for 'labs' sigMatrix,CuffSet: no visible global function definition for 'theme' sigMatrix,CuffSet: no visible global function definition for 'element_text' sigMatrix,CuffSet: no visible global function definition for 'coord_equal' varModel,CuffSet: no visible global function definition for 'dbGetQuery' Undefined global functions or variables: ..n.. ..scaled.. A BiomartGeneRegionTrack CV GRanges GeneRegionTrack GenomeAxisTrack IRanges IdeogramTrack M M1 M2 Rle X1 X2 acast aes aes_string arrow as.dendrogram as.dist as.formula cluster cmdscale colInd compatible_count_mean compatible_count_var condition conf_hi conf_lo coord_equal coord_polar dbBegin dbCommit dbConnect dbDriver dbGetPreparedQuery dbGetQuery dbReadTable dbSendQuery dbWriteTable dcast dispersion dist elementMetadata elementMetadata<- elementNROWS element_blank element_line element_rect element_text end expand_limits facet_grid facet_wrap fitted_var geom_abline geom_bar geom_boxplot geom_density geom_errorbar geom_hex geom_hline geom_line geom_point geom_rect geom_rug geom_segment geom_smooth geom_text geom_tile geom_vline ggplot guides hasAxis<- hclust ids import labs log2_fold_change make.db.names makeTxDb mean_cl_boot melt nnmf obsnames order.dendrogram p.adjust p_value pam plotIdeogram plotTracks position_dodge prcomp quant_status ranges read.delim read.table rowInd sample_1 sample_2 sample_name scale_color_gradient scale_color_hue scale_color_manual scale_colour_manual scale_fill_continuous scale_fill_gradient scale_fill_gradient2 scale_fill_hue scale_x_continuous scale_x_discrete scale_x_log10 scale_y_continuous scale_y_discrete scale_y_log10 sd seqnames significant start stat_density stat_smooth stat_sum stat_summary stdev str_split_fixed strand theme theme_bw toJSON tracking_id tracks unit v1 v2 value values variable varnames write.table x xlab xlim y ylab Consider adding importFrom("stats", "as.dendrogram", "as.dist", "as.formula", "cmdscale", "dist", "end", "hclust", "order.dendrogram", "p.adjust", "prcomp", "sd", "start") importFrom("utils", "read.delim", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in Rd file 'diffData.Rd': ‘...’ Documented arguments not in \usage in Rd file 'distValues.Rd': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Auto-generated content requiring editing in Rd file 'cummeRbund-package.Rd': \references: ‘~~ Literature or other references for background information ~~’ * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/cummeRbund.Rcheck/00check.log’ for details.
cummeRbund.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cummeRbund ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)
cummeRbund.Rcheck/cummeRbund-Ex.timings
name | user | system | elapsed | |
CuffData-class | 0.002 | 0.001 | 0.003 | |
CuffDist-class | 0 | 0 | 0 | |
CuffFeature-class | 0.001 | 0.000 | 0.002 | |
CuffFeatureSet-class | 0.000 | 0.000 | 0.001 | |
CuffGene-class | 0.000 | 0.001 | 0.001 | |
CuffGeneSet-class | 0.001 | 0.001 | 0.002 | |
CuffSet-class | 0.001 | 0.001 | 0.001 | |
JSdist | 0.002 | 0.001 | 0.002 | |
JSdistFromP | 0.001 | 0.001 | 0.001 | |
JSdistVec | 0.001 | 0.001 | 0.001 | |
MAplot | 2.180 | 0.201 | 2.447 | |
PINK1 | 0.009 | 0.003 | 0.012 | |
QCplots | 0.371 | 0.016 | 0.389 | |
addFeatures | 0 | 0 | 0 | |
count | 0.008 | 0.003 | 0.011 | |
countMatrix | 0.019 | 0.004 | 0.023 | |
csBoxplot | 0.562 | 0.064 | 0.640 | |
csCluster | 0.036 | 0.006 | 0.043 | |
csClusterPlot | 0.813 | 0.022 | 0.840 | |
csDendro | 0.018 | 0.003 | 0.021 | |
csDensity | 0.359 | 0.006 | 0.370 | |
csDistHeat | 0.247 | 0.005 | 0.252 | |
csHeatmap | 0.211 | 0.004 | 0.218 | |
csScatter | 0.313 | 0.018 | 0.336 | |
csSpecificity | 0.014 | 0.003 | 0.018 | |
csVolcano | 0.252 | 0.005 | 0.260 | |
diffData | 0.008 | 0.003 | 0.010 | |
dimensionality | 1.888 | 0.016 | 1.914 | |
dispersionPlot | 0.357 | 0.006 | 0.364 | |
distValues | 0.053 | 0.056 | 0.109 | |
exploratory | 0.071 | 0.009 | 0.082 | |
expressionBarplot | 0.623 | 0.012 | 0.640 | |
expressionPlot | 0.676 | 0.011 | 0.691 | |
featureNames | 0.010 | 0.003 | 0.013 | |
features | 0.009 | 0.005 | 0.013 | |
findGene | 0.024 | 0.002 | 0.025 | |
findSimilar | 0.991 | 0.019 | 1.017 | |
fpkm | 0.008 | 0.003 | 0.011 | |
fpkmMatrix | 0.018 | 0.005 | 0.023 | |
getFeatures | 0.019 | 0.002 | 0.023 | |
getGene | 0.102 | 0.007 | 0.109 | |
getGeneId | 0.032 | 0.001 | 0.034 | |
getGenes | 0.084 | 0.008 | 0.093 | |
getSig | 0.014 | 0.002 | 0.015 | |
getSigTable | 0.016 | 0.002 | 0.018 | |
makeprobs | 0 | 0 | 0 | |
makeprobsvec | 0.000 | 0.000 | 0.001 | |
readCufflinks | 0.008 | 0.001 | 0.009 | |
repFpkm | 0.010 | 0.003 | 0.014 | |
replicates | 0.014 | 0.001 | 0.015 | |
runInfo | 0.012 | 0.001 | 0.012 | |
sampleGeneSet | 0.006 | 0.002 | 0.009 | |
sampleIDs | 0.006 | 0.001 | 0.008 | |
samples | 0.011 | 0.001 | 0.012 | |
shannon.entropy | 0 | 0 | 0 | |
sigMatrix | 0.398 | 0.008 | 0.410 | |