BioC 2.13: CHECK report for flowPlots on moscato1

Package: flowPlots

Version: 1.10.0

Command: rm -rf flowPlots.buildbin-libdir && mkdir flowPlots.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowPlots.buildbin-libdir flowPlots_1.10.0.tar.gz >flowPlots-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=flowPlots.buildbin-libdir --install="check:flowPlots-install.out" --force-multiarch --no-vignettes --timings flowPlots_1.10.0.tar.gz && mv flowPlots.buildbin-libdir/* flowPlots.Rcheck/ && rmdir flowPlots.buildbin-libdir

StartedAt: 2014-04-05 03:54:10 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:55:46 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 96.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowPlots.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/flowPlots.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowPlots/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowPlots' version '1.10.0'
* 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 'flowPlots' 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
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'flowPlots.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [23s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
StackedData-class 9.88   0.04   10.08
** running examples for arch 'x64' ... [34s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
StackedData-class 13.59   0.02   14.63
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/flowPlots.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowPlots' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'flowPlots' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowPlots' as flowPlots_1.10.0.zip
* DONE (flowPlots)

name	user	system	elapsed
GroupListBoxplot	0.15	0.00	0.16
StackedData-class	9.88	0.04	10.08
adultsNeonates	0.00	0.02	0.01
computeMarginalData-methods	2.63	0.00	2.64
computeMarkers-methods	0	0	0
computePFDData-methods	2.71	0.00	2.75
computePFDGroupStatsList	0.41	0.01	0.42
computePFDPartsData-methods	2.55	0.00	2.54
computeProfileData-methods	2.76	0.00	2.76
legendPFDStatsGroupNames	0.14	0.00	0.14
makeBarplotData	0.01	0.00	0.01
makeDataList	0.08	0.00	0.08
makeTernaryData	0.14	0.00	0.14
marginalDF	0	0	0
marginalData-methods	0	0	0
markerMatrix	0	0	0
markers-methods	0	0	0
pfdDF	0.01	0.00	0.01
pfdData-methods	0.05	0.00	0.05
pfdPartsData-methods	0.01	0.00	0.02
pfdPartsList	0	0	0
profileDF	0	0	0
profileData-methods	0.01	0.00	0.01
readStackedData-methods	0.13	0.00	0.13
stackedData-methods	0.15	0.00	0.15

name	user	system	elapsed
GroupListBoxplot	0.22	0.00	0.28
StackedData-class	13.59	0.02	14.63
adultsNeonates	0.00	0.01	0.01
computeMarginalData-methods	3.32	0.00	3.39
computeMarkers-methods	0	0	0
computePFDData-methods	3.46	0.00	4.26
computePFDGroupStatsList	0.30	0.03	1.13
computePFDPartsData-methods	4.34	0.00	4.34
computeProfileData-methods	3.90	0.02	3.92
legendPFDStatsGroupNames	0.13	0.02	0.14
makeBarplotData	0.02	0.00	0.02
makeDataList	0.06	0.00	0.06
makeTernaryData	0.09	0.00	0.09
marginalDF	0.02	0.00	0.02
marginalData-methods	0	0	0
markerMatrix	0.01	0.00	0.02
markers-methods	0	0	0
pfdDF	0.02	0.00	0.01
pfdData-methods	0	0	0
pfdPartsData-methods	0	0	0
pfdPartsList	0.01	0.00	0.01
profileDF	0	0	0
profileData-methods	0	0	0
readStackedData-methods	0.1	0.0	0.1
stackedData-methods	0.14	0.00	0.14