Mercurial > repos > devteam > cummerbund
changeset 5:78fcfc04fcfe draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3
| author | devteam |
|---|---|
| date | Thu, 23 Feb 2017 20:24:03 -0500 |
| parents | ba8fde59843d |
| children | c3b54a4b7741 |
| files | cummeRbund.R cummeRbund.xml cummeRbund_macros.xml test-data/boxplot.png test-data/boxplot.txt test-data/cuffdiff_out.sqlite test-data/dendrogram.png test-data/dendrogram.txt test-data/density.png test-data/density.txt test-data/dispersion.png test-data/dispersion.txt test-data/expressionbarplot.png test-data/expressionbarplot.txt test-data/expressionplot.png test-data/expressionplot.txt test-data/fpkmSCV.png test-data/fpkmSCV.txt test-data/heatmap.png test-data/heatmap.txt test-data/maplot.png test-data/maplot.txt test-data/pca.png test-data/pca.txt test-data/scatter.png test-data/scatter.txt test-data/scatterMatrix.png test-data/scatterMatrix.txt test-data/volcano.png test-data/volcano.txt tool_dependencies.xml |
| diffstat | 31 files changed, 977 insertions(+), 1366 deletions(-) [+] |
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--- a/cummeRbund.R Tue Jul 21 14:18:39 2015 -0400 +++ b/cummeRbund.R Thu Feb 23 20:24:03 2017 -0500 @@ -1,4 +1,5 @@ ## Feature Selection ## +options(echo=TRUE) get_features <- function(myGenes, f="gene") { if (f == "isoforms") return(isoforms(myGenes))
--- a/cummeRbund.xml Tue Jul 21 14:18:39 2015 -0400 +++ b/cummeRbund.xml Thu Feb 23 20:24:03 2017 -0500 @@ -1,20 +1,18 @@ <?xml version="1.0"?> -<tool id="cummeRbund" name="cummeRbund" version="1.0.1"> +<tool id="cummeRbund" name="cummeRbund" version="2.16.0"> <description>visualize Cuffdiff output</description> - <requirements> - <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="2.8.2">cummeRbund</requirement> - </requirements> - <expand macro="stdio" /> <macros> <import>cummeRbund_macros.xml</import> </macros> + <requirements> + <requirement type="package" version="1.0.1">r-argparse</requirement> + <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement> + </requirements> <code file="cummeRbund_options.py"/> - <command> + <command detect_errors="aggressive"> <![CDATA[ #for i, p in enumerate($plots): - R --vanilla --no-save -f \$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args + Rscript $__tool_directory__/cummeRbund.R --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}" --outfile plot-${p.plot.type}-${i}.png #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]: @@ -40,6 +38,7 @@ #elif $p.plot.type == "heatmap": --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10 #if len($p.plot.genes) > 0: + --gene_selector #for gene in $p.plot.genes: --genes ${gene.gene_id} #end for @@ -124,7 +123,7 @@ <option value="none">None</option> </param> <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/> - <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display column labels?"/> + <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display row labels?"/> <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/> <expand macro="log10_checkbox" /> </when> @@ -272,7 +271,10 @@ <conditional name="plot"> <param name="type" value="heatmap" /> <repeat name="genes"> - <param name="gene_id" value="XLOC_000078" /> + <param name="gene_id" value="XLOC_000030" /> + </repeat> + <repeat name="genes"> + <param name="gene_id" value="XLOC_000037" /> </repeat> </conditional> </repeat> @@ -353,7 +355,7 @@ ------ -Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute. +Based on the `cummeRbund wrapper <https://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute. ]]></help> <citations> <citation type="doi">doi:10.1038/nprot.2012.016</citation>
--- a/cummeRbund_macros.xml Tue Jul 21 14:18:39 2015 -0400 +++ b/cummeRbund_macros.xml Thu Feb 23 20:24:03 2017 -0500 @@ -1,13 +1,5 @@ <?xml version="1.0"?> <macros> - <macro name="stdio"> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - </macro> <macro name="replicates_checkbox"> <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/> </macro> @@ -19,7 +11,8 @@ <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" /> </macro> <macro name="genes_selector"> - <repeat name="genes" title="Genes"> + <repeat name="genes" title="Genes" min="2"> + <!-- Cannot create a heatmap for less than two genes --> <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" /> </repeat> </macro>
--- a/test-data/boxplot.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/boxplot.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-boxplot-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_34.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "boxplot" - -$replicates -[1] TRUE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,8 +275,5 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file > devname = dev.off() > -> #end for ->
--- a/test-data/dendrogram.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/dendrogram.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-dendrogram-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_43.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "dendrogram" - -$replicates -[1] TRUE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,9 +275,6 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file 'dendrogram' with 2 branches and 2 members total, at height 0.7672512 > devname = dev.off() > -> #end for ->
--- a/test-data/density.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/density.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-density-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmpqBHFSU/tmpJRwxiS/database/files/001/dataset_1450.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] TRUE - -$plotType -[1] "density" - -$replicates -[1] TRUE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,11 +275,7 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file -Warning messages: -1: Removed 65 rows containing non-finite values (stat_density). -2: Removed 63 rows containing non-finite values (stat_density). +Warning message: +Removed 128 rows containing non-finite values (stat_density). > devname = dev.off() > -> #end for ->
--- a/test-data/dispersion.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/dispersion.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-dispersion-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_25.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "dispersion" - -$replicates -[1] FALSE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,8 +275,8 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file +Warning messages: +1: Transformation introduced infinite values in continuous x-axis +2: Transformation introduced infinite values in continuous y-axis > devname = dev.off() > -> #end for ->
--- a/test-data/expressionbarplot.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/expressionbarplot.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] TRUE - -$features -[1] "gene" - -$filename -[1] "plot-expressionbarplot-0.png" - -$gene_selector -[1] FALSE - -$genes -[1] "XLOC_000039" - -$height -[1] 960 - -$input_database -[1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_19.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] TRUE - -$plotType -[1] "expressionbarplot" - -$replicates -[1] TRUE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -331,10 +305,7 @@ distData Getting relCDS information: distData -Scale for 'colour' is already present. Adding another scale for 'colour', which will replace the existing scale. -ymax not defined: adjusting position using y instead -Fontconfig error: Cannot load default config file +Scale for 'colour' is already present. Adding another scale for 'colour', +which will replace the existing scale. > devname = dev.off() > -> #end for ->
--- a/test-data/expressionplot.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/expressionplot.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] TRUE - -$features -[1] "gene" - -$filename -[1] "plot-expressionplot-0.png" - -$gene_selector -[1] FALSE - -$genes -[1] "XLOC_000059" - -$height -[1] 960 - -$input_database -[1] "/tmp/tmpNZmIuK/tmpbebRiN/database/files/000/dataset_94.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] TRUE - -$plotType -[1] "expressionplot" - -$replicates -[1] TRUE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -331,8 +305,5 @@ distData Getting relCDS information: distData -Fontconfig error: Cannot load default config file > devname = dev.off() > -> #end for ->
--- a/test-data/fpkmSCV.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/fpkmSCV.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-fpkmSCV-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_49.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "fpkmSCV" - -$replicates -[1] FALSE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,13 +275,11 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. -geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method. -Fontconfig error: Cannot load default config file +Scale for 'x' is already present. Adding another scale for 'x', which will +replace the existing scale. +`geom_smooth()` using method = 'loess' Warning message: In .local(object, FPKMLowerBound, ...) : At least one of your conditions does not have enough replicates to estimate variance. Estimating variance across all conditions instead. > devname = dev.off() > -> #end for ->
--- a/test-data/heatmap.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/heatmap.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "gene" - -$filename -[1] "plot-heatmap-0.png" - -$gene_selector -[1] FALSE - -$genes -[1] "XLOC_000078" - -$height -[1] 960 - -$input_database -[1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_22.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] TRUE - -$labrow -[1] TRUE - -$log10 -[1] TRUE - -$plotType -[1] "heatmap" - -$replicates -[1] FALSE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -333,8 +307,5 @@ distData Using tracking_id, sample_name as id variables No id variables; using all as measure variables -Fontconfig error: Cannot load default config file > devname = dev.off() > -> #end for ->
--- a/test-data/maplot.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/maplot.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-maplot-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmpk0xwrM/tmpNNuxXE/database/files/000/dataset_1.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "maplot" - -$replicates -[1] FALSE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -[1] "q1" - -$y -[1] "q2" - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,10 +275,7 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file Warning message: Removed 52 rows containing missing values (geom_point). > devname = dev.off() > -> #end for ->
--- a/test-data/pca.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/pca.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-pca-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmpY6OfpX/tmpXqSg_D/database/files/000/dataset_13.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "pca" - -$replicates -[1] TRUE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,8 +275,6 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file +Warning: Ignoring unknown aesthetics: label > devname = dev.off() > -> #end for ->
--- a/test-data/scatter.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/scatter.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-scatter-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmp_cslqP/tmpQijFOJ/database/files/000/dataset_55.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] TRUE - -$plotType -[1] "scatter" - -$replicates -[1] FALSE - -$smooth -[1] TRUE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -[1] "q1" - -$y -[1] "q2" - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,8 +275,5 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file > devname = dev.off() > -> #end for ->
--- a/test-data/scatterMatrix.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/scatterMatrix.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-scatterMatrix-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_28.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "scatterMatrix" - -$replicates -[1] FALSE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -NULL - -$y -NULL - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,8 +275,5 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file > devname = dev.off() > -> #end for ->
--- a/test-data/volcano.txt Tue Jul 21 14:18:39 2015 -0400 +++ b/test-data/volcano.txt Thu Feb 23 20:24:03 2017 -0500 @@ -1,23 +1,3 @@ - -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Copyright (C) 2014 The R Foundation for Statistical Computing -Platform: x86_64-unknown-linux-gnu (64-bit) - -R is free software and comes with ABSOLUTELY NO WARRANTY. -You are welcome to redistribute it under certain conditions. -Type 'license()' or 'licence()' for distribution details. - - Natural language support but running in an English locale - -R is a collaborative project with many contributors. -Type 'contributors()' for more information and -'citation()' on how to cite R or R packages in publications. - -Type 'demo()' for some demos, 'help()' for on-line help, or -'help.start()' for an HTML browser interface to help. -Type 'q()' to quit R. - -> ## Feature Selection ## > get_features <- function(myGenes, f="gene") { + if (f == "isoforms") + return(isoforms(myGenes)) @@ -61,79 +41,10 @@ > > args <- parser$parse_args() > -> print(args) -$border -[1] FALSE - -$clustering -[1] "both" - -$count -[1] FALSE - -$error_bars -[1] FALSE - -$features -[1] "genes" - -$filename -[1] "plot-volcano-0.png" - -$gene_selector -[1] FALSE - -$genes -NULL - -$height -[1] 960 - -$input_database -[1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_46.dat" - -$iter_max -NULL - -$k -NULL - -$labcol -[1] FALSE - -$labrow -[1] FALSE - -$log10 -[1] FALSE - -$plotType -[1] "volcano" - -$replicates -[1] FALSE - -$smooth -[1] FALSE - -$summary -[1] FALSE - -$width -[1] 1280 - -$x -[1] "q1" - -$y -[1] "q2" - -> -> #q() -> > ## Load cummeRbund library > library("cummeRbund") Loading required package: BiocGenerics +Loading required package: methods Loading required package: parallel Attaching package: ‘BiocGenerics’ @@ -144,18 +55,18 @@ clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:stats’: +The following objects are masked from ‘package:stats’: - xtabs + IQR, mad, xtabs The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, - do.call, duplicated, eval, evalq, Filter, Find, get, intersect, - is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, - pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, - rownames, sapply, setdiff, sort, table, tapply, union, unique, - unlist, unsplit + anyDuplicated, append, as.data.frame, cbind, colnames, do.call, + duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, + is.unsorted, lapply, lengths, Map, mapply, match, mget, order, + paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, + Reduce, rownames, sapply, setdiff, sort, table, tapply, union, + unique, unsplit, which, which.max, which.min Loading required package: RSQLite Loading required package: DBI @@ -171,12 +82,75 @@ Loading required package: rtracklayer Loading required package: GenomicRanges +Loading required package: stats4 Loading required package: S4Vectors -Loading required package: stats4 + +Attaching package: ‘S4Vectors’ + +The following objects are masked from ‘package:base’: + + colMeans, colSums, expand.grid, rowMeans, rowSums + Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Gviz Loading required package: grid +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘ensembldb’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ +Warning: namespace ‘AnnotationHub’ is not available and has been replaced +by .GlobalEnv when processing object ‘plot.index’ Attaching package: ‘cummeRbund’ @@ -301,8 +275,5 @@ + write(paste("Failed:", e, sep=" "), stderr()) + q("no", 1, TRUE) + }) -Fontconfig error: Cannot load default config file > devname = dev.off() > -> #end for ->
--- a/tool_dependencies.xml Tue Jul 21 14:18:39 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable action="set_to" name="CUMMERBUND_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="cummeRbund" version="2.8.2"> - <repository changeset_revision="13c270433440" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.1.2"> - <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>