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BioC 2.13: CHECK report for Heatplus on perceval

This page was generated on 2014-04-05 09:51:50 -0700 (Sat, 05 Apr 2014).

Package 341/750HostnameOS / ArchBUILDCHECKBUILD BIN
Heatplus 2.8.0
Alexander Ploner
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Heatplus
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: Heatplus
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Heatplus_2.8.0.tar.gz
StartedAt: 2014-04-05 01:57:54 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:58:36 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 42.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Heatplus.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Heatplus.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Heatplus/DESCRIPTION’ ... OK
* this is package ‘Heatplus’ version ‘2.8.0’
* 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 ‘Heatplus’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
Unexported object imported by a ‘:::’ call: ‘stats:::plotNode’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmap_2: warning in layout(ll, width = ll.width, height = ll.height,
  respect = TRUE): partial argument match of 'width' to 'widths'
heatmap_2: warning in layout(ll, width = ll.width, height = ll.height,
  respect = TRUE): partial argument match of 'height' to 'heights'
heatmap_plus: warning in layout(ll, width = ll.width, height =
  ll.height, respect = TRUE): partial argument match of 'width' to
  'widths'
heatmap_plus: warning in layout(ll, width = ll.width, height =
  ll.height, respect = TRUE): partial argument match of 'height' to
  'heights'
heatmapLayout: warning in layout(ll, width = ll.width, height =
  ll.height, respect = TRUE): partial argument match of 'width' to
  'widths'
heatmapLayout: warning in layout(ll, width = ll.width, height =
  ll.height, respect = TRUE): partial argument match of 'height' to
  'heights'
oldPicketplot: warning in matrix(c(1, 2), nc = 1): partial argument
  match of 'nc' to 'ncol'
oldPicketplot: warning in axis(2, at = yy, label = label, las = TRUE,
  font = 2, col = par("bg"), col.axis = par("fg"), tick = FALSE):
  partial argument match of 'label' to 'labels'
oldPicketplot: warning in axis(2, at = yy, label = label, las = TRUE,
  tick = FALSE, font = 2): partial argument match of 'label' to
  'labels'
oldPicketplot: warning in axis(1, xx.grp, label = FALSE, tcl = -1.5):
  partial argument match of 'label' to 'labels'
oldPicketplot: warning in axis(1, mids, label = grplabel, font = 2,
  cex.axis = cc$cex.label, tick = FALSE): partial argument match of
  'label' to 'labels'
picketPlot: warning in axis(labaxis, at = panels[[i]]$labcc, label =
  panels[[i]]$label, las = las, tick = FALSE, font = 2, col =
  par("bg"), col.axis = par("fg")): partial argument match of 'label'
  to 'labels'
picketPlot: warning in axis(grpaxis, grpcoord, label = FALSE, tcl =
  -1.5): partial argument match of 'label' to 'labels'
picketPlot: warning in axis(grpaxis, mids, label = grplabel, font = 2,
  cex.axis = cc$cex.label, tick = FALSE): partial argument match of
  'label' to 'labels'
annHeatmap2: no visible global function definition for ‘clustfun’
annHeatmap2: no visible global function definition for ‘distfun’
annHeatmap2: no visible binding for global variable ‘cuth’
annHeatmap2: no visible binding for global variable ‘asIs’
annHeatmap2: no visible binding for global variable ‘inclRef’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘annHeatmap.Rnw’, ‘annHeatmapCommentedSource.Rnw’, ‘oldHeatplus.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [9s/9s] OK
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/Heatplus.Rcheck/00check.log’
for details.

Heatplus.Rcheck/00install.out:

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

Heatplus.Rcheck/Heatplus-Ex.timings:

nameusersystemelapsed
RGBColVec0.0510.0060.062
annHeatmap3.2010.1023.346
annHeatmap20.3100.0230.340
breakColors0.0340.0030.038
convAnnData0.1230.0060.134
doLegend0.0090.0000.010
g2r.colors0.0240.0010.026
heatmapLayout0.0130.0020.016
heatmap_22.3350.0522.432
heatmap_plus1.0320.0231.078
modifyExistingList0.0370.0060.045
niceBreaks0.0100.0020.012
oldCutplot.dendrogram0.0660.0020.069
oldPicketplot0.0360.0030.040
picketPlot0.1450.0050.152
plot.annHeatmap0.3600.0190.387
print.annHeatmap0.0450.0010.046
regHeatmap0.0640.0040.071