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BioC 3.4: CHECK report for Heatplus on tokay1

This page was generated on 2017-04-15 16:14:56 -0400 (Sat, 15 Apr 2017).

Package 585/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Heatplus 2.20.0
Alexander Ploner
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Heatplus
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Heatplus
Version: 2.20.0
Command: rm -rf Heatplus.buildbin-libdir Heatplus.Rcheck && mkdir Heatplus.buildbin-libdir Heatplus.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Heatplus.buildbin-libdir Heatplus_2.20.0.tar.gz >Heatplus.Rcheck\00install.out 2>&1 && cp Heatplus.Rcheck\00install.out Heatplus-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Heatplus.buildbin-libdir --install="check:Heatplus-install.out" --force-multiarch --no-vignettes --timings Heatplus_2.20.0.tar.gz
StartedAt: 2017-04-14 22:57:09 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:57:42 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 32.4 seconds
RetCode: 0
Status:  OK  
CheckDir: Heatplus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Heatplus.buildbin-libdir Heatplus.Rcheck && mkdir Heatplus.buildbin-libdir Heatplus.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Heatplus.buildbin-libdir Heatplus_2.20.0.tar.gz >Heatplus.Rcheck\00install.out 2>&1 && cp Heatplus.Rcheck\00install.out Heatplus-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Heatplus.buildbin-libdir --install="check:Heatplus-install.out" --force-multiarch --no-vignettes --timings Heatplus_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/Heatplus.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '2.20.0'
* 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 installed files from 'inst/doc' ... 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
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/Heatplus.Rcheck/00check.log'
for details.


Heatplus.Rcheck/00install.out:


install for i386

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

install for x64

* installing *source* package 'Heatplus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Heatplus' as Heatplus_2.20.0.zip
* DONE (Heatplus)

Heatplus.Rcheck/examples_i386/Heatplus-Ex.timings:

nameusersystemelapsed
BrewerClusterCol0.030.000.03
RGBColVec0.040.000.03
annHeatmap0.820.010.85
annHeatmap20.130.020.14
breakColors000
convAnnData0.040.000.03
doLegend000
g2r.colors000
heatmapLayout000
heatmap_21.160.011.19
heatmap_plus0.580.000.57
modifyExistingList000
niceBreaks000
oldCutplot.dendrogram0.030.000.04
oldPicketplot0.010.000.01
picketPlot0.050.040.08
plot.annHeatmap0.140.010.16
print.annHeatmap0.020.000.01
regHeatmap0.010.000.02

Heatplus.Rcheck/examples_x64/Heatplus-Ex.timings:

nameusersystemelapsed
BrewerClusterCol0.040.000.03
RGBColVec0.000.020.02
annHeatmap0.890.000.89
annHeatmap20.150.010.17
breakColors000
convAnnData0.050.000.05
doLegend0.010.000.01
g2r.colors000
heatmapLayout000
heatmap_21.990.032.02
heatmap_plus0.720.030.75
modifyExistingList000
niceBreaks000
oldCutplot.dendrogram0.060.000.06
oldPicketplot0.030.000.03
picketPlot0.130.020.14
plot.annHeatmap0.250.020.27
print.annHeatmap0.030.000.03
regHeatmap0.030.000.03