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CHECK report for Heatplus on riesling1

This page was generated on 2021-05-10 12:14:11 -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: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Heatplus.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Heatplus_2.37.0.tar.gz
StartedAt: 2021-05-10 00:06:17 -0400 (Mon, 10 May 2021)
EndedAt: 2021-05-10 00:08:35 -0400 (Mon, 10 May 2021)
EllapsedTime: 138.2 seconds
RetCode: 0
Status:   OK   
CheckDir: Heatplus.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Heatplus.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Heatplus_2.37.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/Heatplus.Rcheck'
* using R version 4.1.0 alpha (2021-04-29 r80249)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-bioc/meat/Heatplus.Rcheck/00check.log'
for details.



Installation output

Heatplus.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Heatplus_2.37.0.tar.gz && rm -rf Heatplus.buildbin-libdir && mkdir Heatplus.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Heatplus.buildbin-libdir Heatplus_2.37.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Heatplus_2.37.0.zip && rm Heatplus_2.37.0.tar.gz Heatplus_2.37.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 46953  100 46953    0     0   428k      0 --:--:-- --:--:-- --:--:--  428k

install for i386

* installing *source* package 'Heatplus' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Heatplus'
    finding HTML links ... done
    BrewerClusterCol                        html  
    finding level-2 HTML links ... done

    RGBColVec                               html  
    Undocumented                            html  
    annHeatmap                              html  
    annHeatmap2                             html  
    breakColors                             html  
    convAnnData                             html  
    doLegend                                html  
    g2r.colors                              html  
    heatmapLayout                           html  
    heatmap_2                               html  
    heatmap_plus                            html  
    modifyExistingList                      html  
    niceBreaks                              html  
    oldCutplot.dendrogram                   html  
    oldPicketplot                           html  
    picketPlot                              html  
    plot.annHeatmap                         html  
    print.annHeatmap                        html  
    regHeatmap                              html  
** 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

install for x64

* installing *source* package 'Heatplus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Heatplus' as Heatplus_2.37.0.zip
* DONE (Heatplus)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'Heatplus' successfully unpacked and MD5 sums checked

Tests output


Example timings

Heatplus.Rcheck/examples_i386/Heatplus-Ex.timings

nameusersystemelapsed
BrewerClusterCol0.020.020.06
RGBColVec0.030.000.06
annHeatmap0.910.051.29
annHeatmap20.190.010.27
breakColors0.000.000.02
convAnnData0.040.000.05
doLegend0.020.000.02
g2r.colors0.000.000.01
heatmapLayout0.010.000.01
heatmap_21.100.021.21
heatmap_plus0.510.000.76
modifyExistingList000
niceBreaks000
oldCutplot.dendrogram0.030.000.05
oldPicketplot0.040.000.03
picketPlot0.110.000.12
plot.annHeatmap0.180.000.44
print.annHeatmap0.020.000.02
regHeatmap0.030.000.03

Heatplus.Rcheck/examples_x64/Heatplus-Ex.timings

nameusersystemelapsed
BrewerClusterCol0.010.020.04
RGBColVec0.030.000.03
annHeatmap0.950.031.08
annHeatmap20.110.030.35
breakColors0.000.000.06
convAnnData0.050.000.09
doLegend000
g2r.colors000
heatmapLayout0.000.000.05
heatmap_21.140.001.39
heatmap_plus0.470.021.02
modifyExistingList0.000.010.01
niceBreaks000
oldCutplot.dendrogram0.060.000.09
oldPicketplot0.000.000.03
picketPlot0.090.000.12
plot.annHeatmap0.130.000.23
print.annHeatmap0.020.000.01
regHeatmap0.030.000.03