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BioC 3.4: CHECK report for seqplots on morelia

This page was generated on 2017-04-15 16:25:50 -0400 (Sat, 15 Apr 2017).

Package 1130/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqplots 1.12.0
Przemyslaw Stempor
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/seqplots
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ ERROR ] OK 

Summary

Package: seqplots
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqplots_1.12.0.tar.gz
StartedAt: 2017-04-15 07:58:59 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 08:03:13 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 253.9 seconds
RetCode: 1
Status:  ERROR 
CheckDir: seqplots.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqplots_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/seqplots.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqplots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqplots’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seqplots’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    seqplots   4.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
getPlotSetArray : <anonymous>: no visible global function definition
  for ‘qt’
getSF : <anonymous>: no visible global function definition for ‘approx’
ggHeatmapPlotWrapper: no visible global function definition for
  ‘colorRampPalette’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var2’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var1’
ggHeatmapPlotWrapper: no visible binding for global variable ‘value’
heatmapPlotWrapper: no visible global function definition for
  ‘colorRampPalette’
heatmapPlotWrapper: no visible global function definition for ‘layout’
heatmapPlotWrapper: no visible global function definition for
  ‘capture.output’
heatmapPlotWrapper: no visible global function definition for ‘par’
heatmapPlotWrapper: no visible global function definition for ‘abline’
heatmapPlotWrapper: no visible global function definition for ‘axis’
heatmapPlotWrapper: no visible global function definition for ‘image’
heatmapPlotWrapper: no visible global function definition for ‘rect’
heatmapPlotWrapper: no visible global function definition for ‘title’
heatmapPlotWrapper: no visible global function definition for ‘box’
heatmapPlotWrapper: no visible global function definition for
  ‘plot.new’
imPlot2: no visible global function definition for ‘par’
imPlot2: no visible global function definition for ‘image’
imPlot2: no visible global function definition for ‘rect’
imPlot2: no visible global function definition for ‘axis’
imPlot2: no visible global function definition for ‘box’
imPlot2: no visible binding for global variable ‘mtext’
plotMext: no visible global function definition for ‘par’
plotMext: no visible global function definition for ‘rainbow’
plotMext: no visible global function definition for ‘plot.new’
plotMext: no visible global function definition for ‘rgb’
plotMext: no visible global function definition for ‘axis’
plotMext: no visible global function definition for ‘adjustcolor’
plotMext: no visible global function definition for ‘lines’
plotMext: no visible global function definition for ‘abline’
plotAverage,list: no visible global function definition for ‘par’
plotHeatmap,list: no visible global function definition for ‘par’
plotHeatmap,list: no visible global function definition for ‘kmeans’
plotHeatmap,list: no visible global function definition for ‘hclust’
plotHeatmap,list: no visible global function definition for ‘dist’
plotHeatmap,list: no visible global function definition for ‘cutree’
plotHeatmap,list: possible error in supersom(Hlist, grid =
  class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"), rlen =
  100, toroidal = TRUE): unused argument (toroidal = TRUE)
plotHeatmap,list: no visible global function definition for
  ‘as.dendrogram’
plotHeatmap,list: no visible global function definition for ‘title’
Undefined global functions or variables:
  Var1 Var2 abline adjustcolor approx as.dendrogram axis box
  capture.output colorRampPalette cutree dist hclust image kmeans
  layout lines mtext par plot.new qt rainbow rect rgb title value
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow",
             "rgb")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "mtext", "par", "plot.new", "rect", "title")
  importFrom("stats", "approx", "as.dendrogram", "cutree", "dist",
             "hclust", "kmeans", "qt")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getPlotSetArray 4.294  0.197  17.594
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
         xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec, 
         clspace, pointsize, embed, ggplot, raster, ...)
  7: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters, 
         clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend, 
         xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec, 
         clspace, pointsize, embed, ggplot, raster, ...)
  8: supersom(Hlist, grid = class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"), 
         rlen = 100, toroidal = TRUE)
  
  testthat results ================================================================
  OK: 63 SKIPPED: 0 FAILED: 1
  1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/seqplots.Rcheck/00check.log’
for details.

test-all.Rout.fail:


R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

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.

> library(testthat)
> library(seqplots)
SeqPlots ready, type "run()" to start web interface (GUI) or "?getPlotSetArray" for console mode help.
> 
> message('Runing only command line tests, skipping GUI')
Runing only command line tests, skipping GUI
> test_check("seqplots", filter='1')
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53) --
unused argument (toroidal = TRUE)
1: expect_is(plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing", 
       clstmethod = "ssom"), "data.frame") at testthat/test1.R:53
2: klass(object)
3: paste(class(x), collapse = "/")
4: plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing", clstmethod = "ssom")
5: plotHeatmap(psa$unlist()[1], plotScale = "zscore", sortrows = "increasing", clstmethod = "ssom")
6: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters, 
       clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend, 
       xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec, 
       clspace, pointsize, embed, ggplot, raster, ...)
7: plotHeatmap(plotset$data, main, labels, legend, keepratio, plotScale, sortrows, clusters, 
       clstmethod, include, ssomt1, ssomt2, cex.main, cex.lab, cex.axis, cex.legend, 
       xlab, ylab, autoscale, zmin, zmax, xlim, ln.v, s, indi, o_min, o_max, colvec, 
       clspace, pointsize, embed, ggplot, raster, ...)
8: supersom(Hlist, grid = class::somgrid(xdim = ssomt1, ydim = ssomt2, "hexagonal"), 
       rlen = 100, toroidal = TRUE)

testthat results ================================================================
OK: 63 SKIPPED: 0 FAILED: 1
1. Error: Test getPlotSetArray function and plotting interfaces (@test1.R#53) 

Error: testthat unit tests failed
Execution halted

seqplots.Rcheck/00install.out:

* installing *source* package ‘seqplots’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqplots)

seqplots.Rcheck/seqplots-Ex.timings:

nameusersystemelapsed
MotifSetup-class0.0090.0010.010
getPlotSetArray 4.294 0.19717.594
plot0.4070.0180.439
plotAverage0.5220.0130.539
plotHeatmap0.5050.0130.518
run0.0010.0000.001