BioC 2.13: CHECK report for KCsmart on perceval

Package: KCsmart

Version: 2.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KCsmart_2.20.0.tar.gz

StartedAt: 2014-04-05 02:14:51 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:18:17 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 206.5 seconds

RetCode: 0

Status:  OK

CheckDir: KCsmart.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/KCsmart.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KCsmart/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KCsmart’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘KCsmart’ can be installed ... [6s/6s] 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
* 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
‘library’ or ‘require’ call to ‘siggenes’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘siggenes’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.add2spmc’ ‘.checkMirrorLocs’ ‘.comparativeKcPerms’
  ‘.comparativeKcSiggenes’ ‘.convertCGHbase’ ‘.findCutoffByFdr’
  ‘.findfdrcutoff’ ‘.findPeaks’ ‘.getRegions’ ‘.getSigRegions’
  ‘.makePermutations’ ‘.mirrorData’ ‘.permutedSpm’ ‘.samplePointMatrix’
  ‘.samplePointMatrixOld’ ‘.snr’ ‘.spm2spmc’ ‘.varr’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘KCS.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [136s/138s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
KCsmart-package      35.006  2.331  37.839
getSigRegionsCompKC  17.907  3.188  21.468
compareSpmCollection 16.484  3.365  20.099
calcSpmCollection    15.986  2.876  19.020
plotScaleSpace        8.507  1.173   9.741
findSigLevelFdr       4.638  0.777   5.465
plot                  4.605  0.683   5.393
* 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
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/KCsmart.Rcheck/00check.log’
for details.

* installing *source* package ‘KCsmart’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘write.table’ from package ‘utils’ in package ‘KCsmart’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KCsmart)

name	user	system	elapsed
KCsmart-package	35.006	2.331	37.839
calcSpm	1.954	0.279	2.282
calcSpmCollection	15.986	2.876	19.020
compKc-class	0.003	0.005	0.009
compKcSigRegions-class	0.003	0.005	0.008
compareSpmCollection	16.484	3.365	20.099
findSigLevelFdr	4.638	0.777	5.465
findSigLevelTrad	4.002	0.608	4.645
getSigRegionsCompKC	17.907	3.188	21.468
getSigSegments	3.643	0.738	4.493
idPoints	0.019	0.011	0.035
plot	4.605	0.683	5.393
plotScaleSpace	8.507	1.173	9.741
samplePointMatrix-class	0.019	0.007	0.026
sigSegments-class	0.002	0.004	0.007
spmCollection-class	0.021	0.007	0.028
write.table	3.624	0.487	4.116