BioC 2.13: CHECK report for flowMerge on zin1

Package: flowMerge

Version: 2.10.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings flowMerge_2.10.0.tar.gz

StartedAt: 2014-04-05 01:09:24 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:11:05 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 101.5 seconds

RetCode: 0

Status:  OK

CheckDir: flowMerge.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/flowMerge.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMerge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMerge’ version ‘2.10.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘multicore’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowMerge’ can be installed ... [9s/12s] 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:
  ‘flowClust’ ‘flowCore’ ‘methods’ ‘rrcov’ ‘Rgraphviz’
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
* 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
Packages in Depends field not imported from:
  ‘foreach’ ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ call which should be ‘::’: ‘feature:::featureSignif’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘ENT’
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’:
  ‘flowMerge.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [5s/5s] 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

NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/flowMerge.Rcheck/00check.log’
for details.

* installing *source* package ‘flowMerge’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘flowClust::Map’ when loading ‘flowMerge’
Warning: replacing previous import by ‘flowCore::normalize’ when loading ‘flowMerge’
Warning: replacing previous import by ‘flowCore::sort’ when loading ‘flowMerge’
Creating a generic function for ‘merge’ from package ‘base’ in package ‘flowMerge’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘flowClust::Map’ when loading ‘flowMerge’
Warning: replacing previous import by ‘flowCore::normalize’ when loading ‘flowMerge’
Warning: replacing previous import by ‘flowCore::sort’ when loading ‘flowMerge’
* DONE (flowMerge)

name	user	system	elapsed
NENT	0.008	0.000	0.008
fitPiecewiseLinreg	0.012	0.000	0.010
flowClust.res	0.000	0.004	0.005
flowMerge-package	0.008	0.000	0.007
flowObj	0.004	0.004	0.005
map	0.008	0.004	0.012
merge-methods	0.004	0.000	0.004
merge	0.004	0.000	0.003
pFlowMerge	0.008	0.004	0.023
plot-methods	0.008	0.000	0.006
updateU	0.004	0.000	0.005