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BioC 3.2: CHECK report for flowDensity on moscato1

This page was generated on 2016-04-23 10:20:25 -0700 (Sat, 23 Apr 2016).

Package 356/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowDensity 1.4.0
Mehrnoush Malek
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/flowDensity
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowDensity
Version: 1.4.0
Command: rm -rf flowDensity.buildbin-libdir flowDensity.Rcheck && mkdir flowDensity.buildbin-libdir flowDensity.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowDensity.buildbin-libdir flowDensity_1.4.0.tar.gz >flowDensity.Rcheck\00install.out 2>&1 && cp flowDensity.Rcheck\00install.out flowDensity-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=flowDensity.buildbin-libdir --install="check:flowDensity-install.out" --force-multiarch --no-vignettes --timings flowDensity_1.4.0.tar.gz
StartedAt: 2016-04-23 02:18:44 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:23:48 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 304.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: flowDensity.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf flowDensity.buildbin-libdir flowDensity.Rcheck && mkdir flowDensity.buildbin-libdir flowDensity.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowDensity.buildbin-libdir flowDensity_1.4.0.tar.gz >flowDensity.Rcheck\00install.out 2>&1 && cp flowDensity.Rcheck\00install.out flowDensity-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=flowDensity.buildbin-libdir --install="check:flowDensity-install.out" --force-multiarch --no-vignettes --timings flowDensity_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/flowDensity.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowDensity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowDensity' version '1.4.0'
* 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 'flowDensity' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   4.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.densityGating' '.ellipseGating' 'nmRemove'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'deGate':
deGate
  Code: function(flow.frame, channel, n.sd = 1.5, use.percentile =
                 FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
                 sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
                 tinypeak.removal = 1/25, adjust.dens = 1)
  Docs: function(flow.frame, channel, n.sd = 1.5, use.percentile =
                 FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
                 sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
                 tinypeak.removal = 1/25)
  Argument names in code not in docs:
    adjust.dens

Codoc mismatches from documentation object 'plotDens':
plotDens
  Code: function(flow.frame, channels, col, main, xlab, ylab, pch =
                 ".", s = FALSE, outdir, file.name, ...)
  Docs: function(flow.frame, channels, col, main, xlab, ylab, pch =
                 ".", s = FALSE, outdir, file.name, devn = TRUE, ...)
  Argument names in docs not in code:
    devn
  Mismatches in argument names:
    Position: 11 Code: ... Docs: devn

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'deGate':
  'adjust.dens'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [10s] OK
** running examples for arch 'x64' ... [8s] 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 WARNINGs, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/flowDensity.Rcheck/00check.log'
for details.


flowDensity.Rcheck/00install.out:


install for i386

* installing *source* package 'flowDensity' ...
** 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 'flowDensity' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowDensity' as flowDensity_1.4.0.zip
* DONE (flowDensity)

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

nameusersystemelapsed
CellPopulation-class000
deGate0.470.000.47
flowDensity0.420.030.45
getflowFrame0.640.000.64
nmRemove0.470.001.86
notSubFrame0.300.001.01
plotDens0.250.000.36

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

nameusersystemelapsed
CellPopulation-class000
deGate0.430.030.47
flowDensity0.410.020.42
getflowFrame0.700.010.72
nmRemove0.30.00.3
notSubFrame0.140.000.14
plotDens0.570.000.58