Package: Heatplus

Version: 2.2.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings Heatplus_2.2.0.tar.gz

StartedAt: 2012-04-01 01:36:09 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:36:35 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 25.7 seconds

RetCode: 0

Status:  OK

CheckDir: Heatplus.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Heatplus.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Heatplus/DESCRIPTION' ... OK
* this is package 'Heatplus' version '2.2.0'
* 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 whether package 'Heatplus' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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'
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'
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'
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'
* 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 examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/Heatplus.Rcheck/00check.log'
for details.

* installing *source* package 'Heatplus' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'annHeatmap.Rnw' 
   'annHeatmapCommentedSource.Rnw' 
   'oldHeatplus.Rnw' 
** testing if installed package can be loaded

* DONE (Heatplus)

name	user	system	elapsed
RGBColVec	0.032	0.000	0.030
annHeatmap	2.052	0.028	2.110
annHeatmap2	0.208	0.016	0.241
breakColors	0.008	0.000	0.006
convAnnData	0.068	0.000	0.075
doLegend	0.000	0.000	0.001
g2r.colors	0.004	0.000	0.004
heatmapLayout	0.000	0.000	0.001
heatmap_2	2.148	0.008	2.161
heatmap_plus	0.816	0.000	0.818
modifyExistingList	0.004	0.000	0.001
niceBreaks	0.000	0.000	0.001
oldCutplot.dendrogram	0.056	0.000	0.058
oldPicketplot	0.012	0.000	0.014
picketPlot	0.136	0.000	0.139
plot.annHeatmap	0.228	0.008	0.253
print.annHeatmap	0.024	0.000	0.023
regHeatmap	0.036	0.000	0.038