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CHECK report for Heatplus on malbec2

This page was generated on 2019-10-16 11:56:02 -0400 (Wed, 16 Oct 2019).

Package 747/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Heatplus 2.30.0
Alexander Ploner
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Heatplus
Branch: RELEASE_3_9
Last Commit: 9df1904
Last Changed Date: 2019-05-02 11:53:06 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Heatplus
Version: 2.30.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Heatplus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Heatplus_2.30.0.tar.gz
StartedAt: 2019-10-16 02:18:50 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:19:13 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 23.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Heatplus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Heatplus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Heatplus_2.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Heatplus.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Heatplus/DESCRIPTION’ ... OK
* this is package ‘Heatplus’ version ‘2.30.0’
* 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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/Heatplus.Rcheck/00check.log’
for details.



Installation output

Heatplus.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Heatplus
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Heatplus’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Heatplus)

Tests output


Example timings

Heatplus.Rcheck/Heatplus-Ex.timings

nameusersystemelapsed
BrewerClusterCol0.0310.0000.031
RGBColVec0.0190.0000.018
annHeatmap0.7320.0200.751
annHeatmap20.1330.0000.133
breakColors0.0040.0000.004
convAnnData0.0500.0000.116
doLegend0.0020.0000.002
g2r.colors0.0050.0000.005
heatmapLayout0.0030.0000.003
heatmap_21.4700.0121.482
heatmap_plus0.8630.0040.867
modifyExistingList0.0020.0000.002
niceBreaks000
oldCutplot.dendrogram0.050.000.05
oldPicketplot0.0180.0000.018
picketPlot0.1190.0040.123
plot.annHeatmap0.1550.0000.155
print.annHeatmap0.0150.0000.015
regHeatmap0.0230.0000.023