Back to Multiple platform build/check report for BioC 3.13
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

CHECK report for Heatplus on machv2

This page was generated on 2021-05-10 12:14:37 -0400 (Mon, 10 May 2021).

To the developers/maintainers of the Heatplus package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 839/2016HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Heatplus 2.37.0  (landing page)
Alexander Ploner
Snapshot Date: 2021-05-09 14:50:05 -0400 (Sun, 09 May 2021)
URL: https://git.bioconductor.org/packages/Heatplus
Branch: master
Last Commit: 8758c8c
Last Changed Date: 2020-10-27 10:28:24 -0400 (Tue, 27 Oct 2020)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Heatplus
Version: 2.37.0
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_2.37.0.tar.gz
StartedAt: 2021-05-10 03:15:40 -0400 (Mon, 10 May 2021)
EndedAt: 2021-05-10 03:16:17 -0400 (Mon, 10 May 2021)
EllapsedTime: 37.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Heatplus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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_2.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Heatplus.Rcheck’
* using R version 4.1.0 alpha (2021-04-29 r80247)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Heatplus/DESCRIPTION’ ... OK
* this is package ‘Heatplus’ version ‘2.37.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... OK
* 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-3.13-bioc/meat/Heatplus.Rcheck/00check.log’
for details.



Installation output

Heatplus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Heatplus
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
BrewerClusterCol0.0560.0040.061
RGBColVec0.0270.0060.033
annHeatmap1.3450.0611.410
annHeatmap20.2010.0080.210
breakColors0.0060.0010.008
convAnnData0.0600.0050.066
doLegend0.0010.0010.002
g2r.colors0.0060.0020.008
heatmapLayout0.0020.0010.003
heatmap_21.8970.0382.008
heatmap_plus0.9450.0220.972
modifyExistingList0.0020.0020.003
niceBreaks0.0020.0000.002
oldCutplot.dendrogram0.0600.0020.062
oldPicketplot0.0200.0020.023
picketPlot0.1490.0080.157
plot.annHeatmap0.2840.0110.297
print.annHeatmap0.0380.0010.038
regHeatmap0.0530.0010.054