Package: Heatplus

Version: 2.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Heatplus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Heatplus_2.29.0.tar.gz

StartedAt: 2019-04-09 01:27:35 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:28:05 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 30.2 seconds

RetCode: 0

Status:  OK

CheckDir: Heatplus.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Heatplus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Heatplus_2.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Heatplus.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Heatplus/DESCRIPTION’ ... OK
* this is package ‘Heatplus’ version ‘2.29.0’
* 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 ... 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.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  annHeatmap.ExpressionSet annHeatmap.default plot.annHeatmap
  print.annHeatmap regHeatmap.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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'
BrewerClusterCol: no visible binding for global variable ‘category’
annHeatmap.ExpressionSet: no visible global function definition for
  ‘exprs’
annHeatmap.ExpressionSet: no visible global function definition for
  ‘pData’
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’
convAnnData: no visible global function definition for ‘na.exclude’
convAnnData: no visible global function definition for ‘model.matrix’
convAnnData: no visible global function definition for ‘naresid’
cutplot.dendrogram: no visible global function definition for
  ‘segments’
getLeaves: no visible global function definition for ‘dendrapply’
heatmapLayout: no visible global function definition for ‘layout.show’
print.annHeatmap: no visible global function definition for ‘show’
Undefined global functions or variables:
  asIs category clustfun cuth dendrapply distfun exprs inclRef
  layout.show model.matrix na.exclude naresid pData segments show
Consider adding
  importFrom("graphics", "layout.show", "segments")
  importFrom("methods", "show")
  importFrom("stats", "dendrapply", "model.matrix", "na.exclude",
             "naresid")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Heatplus.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Heatplus
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Heatplus’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Heatplus)

name	user	system	elapsed
BrewerClusterCol	0.043	0.003	0.047
RGBColVec	0.030	0.003	0.033
annHeatmap	1.028	0.057	1.100
annHeatmap2	0.182	0.007	0.189
breakColors	0.007	0.001	0.009
convAnnData	0.062	0.003	0.065
doLegend	0.001	0.000	0.001
g2r.colors	0.004	0.001	0.004
heatmapLayout	0.002	0.001	0.003
heatmap_2	1.850	0.021	1.897
heatmap_plus	0.779	0.009	0.798
modifyExistingList	0.002	0.001	0.004
niceBreaks	0.001	0.000	0.002
oldCutplot.dendrogram	0.054	0.002	0.055
oldPicketplot	0.022	0.002	0.023
picketPlot	0.122	0.003	0.126
plot.annHeatmap	0.260	0.012	0.272
print.annHeatmap	0.031	0.000	0.032
regHeatmap	0.054	0.001	0.055