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BioC 3.1: CHECK report for flowViz on moscato2

This page was generated on 2015-10-09 09:27:48 -0700 (Fri, 09 Oct 2015).

Package 350/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowViz 1.32.0
Mike Jiang
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/flowViz
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: flowViz
Version: 1.32.0
Command: rm -rf flowViz.buildbin-libdir flowViz.Rcheck && mkdir flowViz.buildbin-libdir flowViz.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowViz.buildbin-libdir flowViz_1.32.0.tar.gz >flowViz.Rcheck\00install.out 2>&1 && cp flowViz.Rcheck\00install.out flowViz-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=flowViz.buildbin-libdir --install="check:flowViz-install.out" --force-multiarch --no-vignettes --timings flowViz_1.32.0.tar.gz
StartedAt: 2015-10-09 01:49:40 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:53:48 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 247.6 seconds
RetCode: 0
Status:  OK  
CheckDir: flowViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowViz.buildbin-libdir flowViz.Rcheck && mkdir flowViz.buildbin-libdir flowViz.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowViz.buildbin-libdir flowViz_1.32.0.tar.gz >flowViz.Rcheck\00install.out 2>&1 && cp flowViz.Rcheck\00install.out flowViz-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=flowViz.buildbin-libdir --install="check:flowViz-install.out" --force-multiarch --no-vignettes --timings flowViz_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/flowViz.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowViz' version '1.32.0'
* 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 'flowViz' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'flowCore' 'lattice'
A package should be listed in only one of these fields.
* 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 objects imported by ':::' calls:
  'flowCore:::findTimeChannel' 'flowCore:::prepareSet'
  'lattice:::updateList'
  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
flowPlot,flowFrame : .local: warning in log(xd, b = 10): partial
  argument match of 'b' to 'base'
flowPlot,flowFrame : .local: warning in log(yd, b = 10): partial
  argument match of 'b' to 'base'
.densityplot.flowSet: no visible global function definition for
  'lattice.getOption'
.xyplot.flowSet: no visible global function definition for 'bwplot'
panel.xyplot.flowframe: no visible global function definition for
  'lpoints'
panel.xyplot.flowframe.old: no visible global function definition for
  'lpoints'
glpoints,filter-flowFrame-missing : .local: no visible binding for
  global variable 'parms'
glpoints,filter-flowFrame-missing : .local: no visible binding for
  global variable 'strict'
gpoints,quadGate-flowFrame-character : .local: no visible binding for
  global variable 'filterResult'
gpolygon,ellipsoidGate-character : .local: no visible binding for
  global variable 'fd'
parallel,flowFrame-missing : .local: no visible global function
  definition for 'parallelplot'
* 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' ... [79s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
densityplot            15.02   0.15   15.56
xyplot                 13.36   0.10   13.56
splom                  12.93   0.19   13.26
latticeMethods-flowSet 11.92   0.31   12.34
timeLinePlot-methods    8.22   0.01    8.23
ecdfplot                7.59   0.02    7.62
** running examples for arch 'x64' ... [80s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
xyplot                 14.05   0.20   14.99
densityplot            13.52   0.42   14.04
latticeMethods-flowSet 13.11   0.27   13.36
splom                  13.07   0.14   13.92
timeLinePlot-methods    7.86   0.02    7.89
ecdfplot                7.16   0.07    7.23
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/flowViz.Rcheck/00check.log'
for details.


flowViz.Rcheck/00install.out:


install for i386

* installing *source* package 'flowViz' ...
** 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 'flowViz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowViz' as flowViz_1.32.0.zip
* DONE (flowViz)

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

nameusersystemelapsed
contour-methods2.270.072.34
densityplot15.02 0.1515.56
ecdfplot7.590.027.62
flowPlot1.140.041.49
flowViz-package000
flowViz.par.get1.920.021.94
latticeMethods-flowSet11.92 0.3112.34
splom12.93 0.1913.26
timeLinePlot-methods8.220.018.23
xyplot13.36 0.1013.56

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

nameusersystemelapsed
contour-methods2.400.042.45
densityplot13.52 0.4214.04
ecdfplot7.160.077.23
flowPlot1.120.031.15
flowViz-package000
flowViz.par.get1.640.041.69
latticeMethods-flowSet13.11 0.2713.36
splom13.07 0.1413.92
timeLinePlot-methods7.860.027.89
xyplot14.05 0.2014.99